Small-molecule mediated size selection of nucleic acids

ABSTRACT

Provided are methods and compositions for negatively and positively selecting for different size nucleic acid (e.g., DNA or RNA) fragments on borosilicate glass fiber membranes, silica and metal oxide surfaces such that only those fragments falling within a desired size range are obtained.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority from U.S. Provisional Application No.62/214,862, filed Sep. 4, 2015, the contents of which are incorporatedby reference herein in their entirety.

FIELD

In some aspects, provided herein are methods and compositions (e.g.,kits) for the size-selective isolation of nucleic acids (e.g., DNA orRNA) from a nucleic acid-containing sample. In particular embodiments,disclosed herein are methods and compositions for small-moleculemediated size selection of nucleic acids on a borosilicate glass,silica, or metal oxide surfaces.

BACKGROUND

The selective fractionation of nucleic acids (e.g., DNA or RNA) by sizeis an important tool in molecular biology. There is an increasinginterest and need for fast, simple and reliable methods for removingundesired nucleic acid fragments from samples in the preparation ofnucleic acid sequencing libraries, such as for next generationsequencing (NGS). The difference in size of nucleic acids is animportant criterion in distinguishing nucleic acids of interest fromnucleic acid byproducts that should be excluded.

Nucleic acids of a specific minimum and/or maximum size are used innucleic acid library construction methods, such as for next generationsequencing applications. To ensure high quality sequencing data,efficient library preparation methods are required to reduce thebackground in the sequencing reads. Therefore, it is important to removenucleic acid contaminants that might be present in the sample as aresult of the library preparation. For example, small nucleic acidmolecules such as adapter monomers and adapter-adapter ligation productsthat are often present in the sequencing library after adapter ligationmust be removed prior to sequencing to reduce background in thesequencing data.

Existing methods of size-selective nucleic acid isolation are cumbersomeand time-consuming. Standard methods for isolating nucleic acidmolecules of a specific target size involve separation of the nucleicacid using gel electrophoresis, cutting out the gel band with thedesired nucleic acid fragment size, and then extracting the nucleic acidmolecules of the specific target size from the gel fragment.

Polyethylene glycol (PEG)-based buffers are also widely used in thesize-selective isolation of nucleic acid fragments. However, PEG-basedisolation methods are disadvantageous because of the highly viscouspolyethylene glycol, which hinders the efficiency of washing the nucleicacids. Size selection of DNA fragments on carboxylic acid-coatedmagnetic beads driven by PEG/NaCl solutions is a well-known technique(U.S. Pat. No. 5,705,628, U.S. Pat. No. 5,898,071, and U.S. Pat. No.6,534,262). However, there is a risk of bead carry-over, which may havea disadvantageous impact on downstream reactions such as subsequentenzymatic reactions. Accordingly, there is a need for additional methodsfor selective fractionation of nucleic acids by size.

SUMMARY

In one aspect, provided is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range. In some embodiments, the method includes contacting a samplecomprising nucleic acid molecules with a matrix in the presence of acarboxylate compound. In some embodiments, the carboxylate compound ispresent in sufficient concentration that the target nucleic acidmolecules selectively bind to the matrix and non-target nucleic acidmolecules do not bind to the matrix.

In some embodiments, greater than about 95% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules. Insome embodiments, greater than about 90% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules. Inother embodiments, greater than about 70% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules.

In some embodiments, the method further includes a step wherein thematrix is washed to remove the unbound nucleic acid. In someembodiments, the method further includes a step wherein the boundnucleic acid molecules are eluted from the matrix.

In some embodiments, the matrix contains silica. In some embodiments,the matrix contains borosilicate glass. In some embodiments, the matrixcontains silicon dioxide. In some embodiments, the matrix containssilicon dioxide-coated magnetic beads. In other embodiments, the matrixcontains a metal oxide.

In some embodiments, the carboxylate compound is of formula (I)

wherein

-   -   R is selected from the group consisting of H, substituted or        unsubstituted C₁-C₈ alkyl, substituted or unsubstituted C₁-C₈        alkenyl, and substituted or unsubstituted C₁-C₈ alkynyl;    -   M is a metal or N(R^(a))₄;    -   each R^(a) is independently H or alkyl; and    -   n is 1, 2, or 3;    -   or a hydrate thereof.

In some embodiments, M^(n+) is Na⁺, Li⁺, K⁺, Ca²⁺, Mg²⁺, Al³⁺, or NH₄ ⁺.In some embodiments, R is substituted or unsubstituted C₁-C₈ alkyl. Insome embodiments, R is CH₃. In some embodiments, R is C₁-C₈ alkylsubstituted with one or more halogen.

In some embodiments, the carboxylate compound contains acetate. In someembodiments, the carboxylate compound is ammonium acetate or sodiumacetate.

In some embodiments, the carboxylate compound is in a solution. In someembodiments, the solution further contains guanidine hydrochloride, TrisHCl, and isopropanol.

In some embodiments, the nucleic acid contains DNA. In otherembodiments, the nucleic acid contains RNA.

In another aspect, provided is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range, the method including:

-   -   a) contacting a sample containing nucleic acid molecules with a        first matrix in the presence of a first carboxylate compound,

wherein the first carboxylate compound is present in sufficientconcentration that nucleic acid molecules of molecular size above theupper limit of the target molecular size range selectively bind to thematrix and nucleic acid molecules of molecular size below the upperlimit of the target molecular size range do not bind to the matrix;

-   -   b) collecting all or a portion of the sample that is not bound        to the first matrix;    -   c) contacting all or the portion of the sample that is not bound        to the first matrix with a second matrix in the presence of a        second carboxylate compound,

wherein the second carboxylate compound is present in a sufficientconcentration that nucleic acid molecules of the target molecular sizerange selectively bind to the second matrix and nucleic acid moleculesof molecular size below the lower limit of the target molecular sizerange do not bind to the matrix.

In some embodiments, the concentration of the first carboxylate compoundis greater than the concentration of the second carboxylate compound. Insome embodiments, the nucleic acid molecules of molecular size above theupper limit of the target molecular size range are removed from thefirst matrix by washing or elution to produce the second matrix.

In another aspect, provided is a kit containing a carboxylate compound,a matrix, and instructions for use according to any of the methodsdescribed herein.

In another aspect, provided is a kit containing ammonium acetate,guanidine hydrochloride, and Tris HCl. In some embodiments, the ammoniumacetate, guanidine hydrochloride, and Tris HCl are present in asolution. In some embodiments, the kit contains about 7.5 M ammoniumacetate, about 5.2 M guanidine hydrochloride, and about 30 mM Tris HCl.In some embodiments, the kit includes a matrix. In some embodiments, thekit includes isopropanol. In some embodiments, the kit includesinstructions for use according to any of the methods described herein.

In another aspect, provided is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range, wherein the method includes contacting a sample comprisingnucleic acid molecules with a matrix in the presence of a small-moleculemodulator, wherein the small-molecule modulator is present in sufficientconcentration that the target nucleic acid molecules selectively bind tothe matrix and non-target nucleic acid molecules do not bind to thematrix.

In some embodiments, greater than about 95% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules. Insome embodiments, greater than about 90% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules. Insome embodiments, greater than about 70% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules.

In some embodiments, the method further includes a step wherein thematrix is washed to remove the unbound nucleic acid. In someembodiments, the method further includes a step wherein the boundnucleic acid molecules are eluted from the matrix. In some embodiments,the matrix contains silica. In some embodiments, the matrix containsborosilicate glass. In some embodiments, the matrix contains silicondioxide. In some embodiments, the matrix contains silicon dioxide-coatedmagnetic beads. In some embodiments, the matrix contains a metal oxide.

In some embodiments, the small-molecule modulator contains a carboxylatemoiety. In some embodiments, the small-molecule modulator contains aphosphate, phosphonate, or borate moiety. In some embodiments, thesmall-molecule modulator contains an ammonium or substituted ammoniummoiety. In some embodiments, the small-molecule modulator is of formula(Ia)

wherein R¹ is a structural moiety that satisfies the following twoconditions: 1) R¹ does not render the carboxylate insoluble in water athigh concentration (preferably 1-8 M); and 2) R¹ cannot be ionized to anegative species within the range of pH 4-9; M is a metal or N(R^(a))₄;each R^(a) is independently H or alkyl; and n is 1, 2, or 3; or ahydrate thereof.

In some embodiments, the small-molecule modulator is of formula (Ib)

wherein R² is a phosphate or a phosphonic acid (e.g., phosphonoaceticacid); M is a metal or N(R^(a))₄; each R^(a) is independently H oralkyl; and n is 1, 2, or 3; or a hydrate thereof.

In some embodiments, the small-molecule modulator is a carboxylatecompound of formula (I)

wherein R is selected from the group consisting of H, substituted orunsubstituted C₁-C₈ alkyl, substituted or unsubstituted C₁-C₈ alkenyl,and substituted or unsubstituted C₁-C₈ alkynyl; M is a metal orN(R^(a))₄; each R^(a) is independently H or alkyl; and n is 1, 2, or 3;or a hydrate thereof. In some embodiments, R is substituted orunsubstituted C₁-C₈ alkyl. In some embodiments, R is CH₃. In someembodiments, R is C₁-C₈ alkyl substituted with one or more halogen.

In some embodiments, M^(n+) is Na⁺, Li⁺, K⁺, Ca²⁺, Mg²⁺, Al³⁺, or NH₄ ⁺.In some embodiments, the small-molecule modulator comprises acetate. Insome embodiments, the small-molecule modulator is ammonium acetate orsodium acetate. In some embodiments, the small-molecule modulator is ina solution. In some embodiments, the solution further comprisesguanidine hydrochloride, Tris-HCl, and isopropanol.

In some embodiments, the nucleic acid comprises DNA. In someembodiments, the nucleic acid comprises RNA.

In another aspect, provided is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range, the method including a) contacting a sample comprisingnucleic acid molecules with a first matrix in the presence of a firstsmall-molecule modulator, wherein the first small-molecule modulator ispresent in sufficient concentration that nucleic acid molecules ofmolecular size above the upper limit of the target molecular size rangeselectively bind to the first matrix and nucleic acid molecules ofmolecular size below the upper limit of the target molecular size rangedo not bind to the first matrix; b) collecting all or a portion of thesample that is not bound to the first matrix; c) contacting all or theportion of the sample that is not bound to the first matrix with asecond matrix in the presence of a second small-molecule modulator,wherein the second small-molecule modulator is present in a sufficientconcentration that nucleic acid molecules of the target molecular sizerange selectively bind to the second matrix and nucleic acid moleculesof molecular size below the lower limit of the target molecular sizerange do not bind to the second matrix.

In some embodiments, the first small-molecule modulator is a carboxylatecompound. In some embodiments, the second small-molecule modulator is acarboxylate compound. In some embodiments, the concentration of thefirst small-molecule modulator is greater than the concentration of thesecond small-molecule modulator. In some embodiments, the nucleic acidmolecules of molecular size above the upper limit of the targetmolecular size range are removed from the first matrix by washing orelution to produce the second matrix.

In another aspect, provided is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range, the method including: a) contacting a sample containingnucleic acid molecules with a first matrix in the absence of asmall-molecule modulator such that both target and non-target nucleicacid molecules bind to the matrix; b) washing the matrix in the presenceof a first small-molecule modulator, wherein the first small-moleculemodulator is present in sufficient concentration that nucleic acidmolecules of molecular size above the upper limit of the targetmolecular size range are selectively retained on the first matrix andnucleic acid molecules of molecular size below the upper limit of thetarget molecular size range are released from the first matrix; c)collecting all or a portion of the sample that is released from thefirst matrix; d) contacting all or the portion of the sample that isreleased from the first matrix with a second matrix in the presence of asecond small-molecule modulator, wherein the second small-moleculemodulator is present in a sufficient concentration that nucleic acidmolecules of the target molecular size range selectively bind to thesecond matrix and nucleic acid molecules of molecular size below thelower limit of the target molecular size range do not bind to the secondmatrix.

In some embodiments, the first small-molecule modulator is a carboxylatecompound. In some embodiments, the second small-molecule modulator is acarboxylate compound. In some embodiments, the concentration of thefirst small-molecule modulator is greater than the concentration of thesecond small-molecule modulator.

In another aspect, provided is a kit containing a small-moleculemodulator, a matrix, and instructions for use according to any of themethods provided herein. In some embodiments, the small-moleculemodulator is a carboxylate compound.

In another aspect, provided is a kit containing ammonium acetate,guanidine hydrochloride, and Tris HCl. In some embodiments, the ammoniumacetate, guanidine hydrochloride, and Tris HCl are present in asolution. In some embodiments, the kit contains about 7.5 M ammoniumacetate, about 5.2 M guanidine hydrochloride, about 30 mM Tris HCl. Insome embodiments, the kit further contains a matrix. In someembodiments, the kit further contains isopropanol. In some embodiments,the kit further contains instructions for use according to any of themethods provided herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 compares the electrophoretic separation of a 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in theabsence of a DNA bind modifier (i.e., bands labeled “Bind only”) and inthe presence of the DNA bind modifier ammonium acetate (i.e., bandslabeled “Bind & −2”).

FIG. 2 compares the electrophoretic separation of a 1 kb DNA molecularweight ladder subjected to an increasing amount of ammonium acetateduring the binding reaction using borosilicate glass spin filters. Thevarious ratios displayed on the gel (e.g., 5/110, 10/120) correspond tothe volume (μL) of 7.5 M ammonium acetate to the volume (μL) of DNAbinding buffer (5.2 M guanidine hydrochloride, 30 mM Tris-HCl, 8%isopropanol).

FIG. 3 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to an increasing amount of ammoniumacetate during the binding reaction using borosilicate glass spinfilters. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while ammonium acetate volumes were varied from 0 to35 μL.

FIG. 4 compares electrophoretic separation of 1 kb DNA molecular weightladder samples contacted with silica-coated magnetic beads (SwiftMag®beads) in the presence or absence of ammonium acetate and in thepresence or absence of DNA binding solution (“Spin Bind”). In the panellabeled “EtOH”, Spin Bind was substituted with an equal volume of 100%ethanol, with or without ammonium acetate (“−2”). In the right panel(“Spin Bind”), DNA binding solution (5.2 M guanidine hydrochloride, 30mM Tris HCl, 8% isopropanol) was used with or without ammonium acetate.50 μL of DNA ladder was combined with 200 μL DNA Binding Solution (orethanol) and L ammonium acetate.

FIG. 5 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples contacted with silica-coated magnetic beads in thepresence of different DNA bind modifiers. Ammonium acetate, lithiumacetate, water, potassium acetate, ammonium chloride, and sodium methanesulfonate were used as DNA bind modifiers. 50 μL of DNA ladder wascombined with 200 μL of DNA Binding Solution and 25 μL of the abovecompounds.

FIG. 6A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium acetate, and lithium acetate were usedas DNA bind modifiers. In this gel, the nucleic acid binding solutionwas held constant at 170 μL while DNA bind modifier volumes were variedfrom 0 to 35 μL.

FIG. 6B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, cesium acetate, ribidium acetate, andpotassium acetate were used as DNA bind modifiers. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 35 μL.

FIG. 7A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. 7.5 M Ammonium acetate, 6.3 M tetramethyl ammonium acetate, and3.44 M tetramethyl ammonium acetate tetrahydrate were used as DNA bindmodifiers. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while DNA bind modifier volumes were varied from 0 to35 μL.

FIG. 7B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. 7.5 M Ammonium acetate, 3.12 M tetramethyl ammonium acetate,4.67 M tetramethyl ammonium acetate, and 6.23 M tetramethyl ammoniumacetate were used as DNA bind modifiers. In this gel, the nucleic acidbinding solution was held constant at 170 μL while DNA bind modifiervolumes were 0, 25, and 35 μL.

FIG. 8A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of different DNA bindmodifiers during the binding reaction using borosilicate glass spinfilters. Sample A contains the 1 kb DNA molecular weight ladder samplein the absence of any DNA bind modifiers. Tetramethyl ammonium acetate(4.7 M), ammonium phosphate dibasic (4.03 M), choline chloride (5.68 M),Tris(2-hydroxyethyl)methylammonium methylsulfate (TMAMS), and ammoniumsulfate (4.4 M) were used as DNA bind modifiers. 50 μL of DNA ladder wascombined with 170 μL of nucleic acid binding solution and 35 μL of theabove compounds.

FIG. 8B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of increasing amounts ofdiammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. 2.02 M DAP and 2.42 M DAP were used asDNA bind modifiers. 50 μL of DNA ladder was combined with 170 μL ofnucleic acid binding solution and DAP volumes were varied from 0 to 35μL.

FIG. 8C compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of diammonium phosphate(DAP) during the binding reaction using borosilicate glass spin filterssubject to selection and different stages. 2.42 M DAP was used as DNAbind modifier in samples B, C, and D. Sample A contained the 1 kb DNAmolecular weight ladder sample in the absence of any DNA bind modifiers.Samples B was 1 kb DNA molecular weight ladder passed through aborosilicate glass spin filter in the presence of 35 μL of 2.42 M DAP.Sample C was the recovered flow through of 1 kb DNA molecular weightladder passed through a borosilicate glass spin filter in the presenceof 35 μL of 2.42 M DAP mixed with ethanol. Sample D contained the 1 kbDNA molecular weight ladder sample in the absence of any DNA bindmodifiers bound to the filter that was then subjected to selection with35 μL of 2.42 M DAP (‘on-filter selection’).

FIG. 9A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the binding reaction using borosilicate glass spin filterssubject to one or more steps of selection. Sample A contained the 1 kbDNA molecular weight ladder sample in the absence of any DNA bindmodifiers. In samples B, C, D, and E, 4.7 M tetramethyl ammonium acetatewas used as DNA bind modifier. Samples B and C were 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in thepresence of 35 μL and 25 μL, respectively, of 4.7 M tetramethyl ammoniumacetate. Sample D was the recovered flow through of 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in thepresence of 35 μL of 4.7 M tetramethyl ammonium acetate (Sample B); theflow through was bound to a spin filter with ethanol, washed and eluted.Sample E was the flow through of 1 kb DNA molecular weight ladder passedthrough a borosilicate glass spin filter in the presence of 35 μL of 4.7M tetramethyl ammonium acetate; the collected flow through was bound toa spin filter with ethanol, as in Sample D, and subjected to a secondstep of selection with 25 μL of 4.7 M tetramethyl ammonium acetate.

FIG. 9B compares electrophoretic separation of 1 kb DNA molecular weightladder samples contacted with silica-coated magnetic beads (SwiftMag®beads) in the presence or absence of 4.7 M tetramethyl ammonium acetatesubject to one or more steps of selection. Tetramethyl ammonium acetateat 4.7 M was used as DNA bind modifier in samples B, C, D, and E.Samples B and C were 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence of 20 μL and 25 μL,respectively, of 4.7 M tetramethyl ammonium acetate. Sample D was therecovered supernatant of 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence of 25 μL of 4.7 Mtetramethyl ammonium acetate. Sample E was the recovered supernatant of1 kb DNA molecular weight ladder contacted with silica-coated magneticbeads in the presence of 25 μL of 4.7 M tetramethyl ammonium acetatethat was then washed and subjected to a second step of selection with 20μL of 4.7 M tetramethyl ammonium acetate.

FIG. 10A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier (ammonium acetate) during the binding reaction usingborosilicate glass spin filters. The amount of ammonium acetate was notnormalized against a standard volume of the nucleic binding buffer. Inthis gel, the nucleic acid binding solution was held constant at 170 μLwhile DNA bind modifier volumes were varied from 0 to 35 μL.

FIG. 10B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier (ammonium acetate) during the binding reaction usingborosilicate glass spin filters. The amount of nucleic acid bindingbuffer and ammonium acetate was normalized against a standard volumeusing water. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while DNA bind modifier volumes were varied from 0 to35 μL.

FIG. 11A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium formate, and sodium propionate wereused as DNA bind modifiers. In this gel, the nucleic acid bindingsolution was held constant at 170 μL while DNA bind modifier volumeswere varied from 0 to 35 μL.

FIG. 11B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium trifluoroacetate, and sodiumtrichloroacetate were used as DNA bind modifiers. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 35 μL.

FIG. 12 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different DNA binding buffers in thepresence or absence of DNA bind modifier (4.67 M tetramethyl ammoniumacetate) during the binding reaction using borosilicate glass spinfilters. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while DNA bind modifier volumes were varied from 0 to35 μL.

FIG. 13 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different DNA binding solutions inthe presence or absence of DNA bind modifier (4.67 M tetramethylammonium acetate) during the binding reaction using borosilicate glassspin filters. Guanidine carbonate, guanidine phosphate, guanidinesulfate, and guanidine thiocyanate based solutions were used as DNAbinding solutions. In this gel, the nucleic acid binding solution washeld constant at 170 μL, DNA bind modifier volumes was either 0 or 35μL.

FIG. 14 compares the electrophoretic separation of 1 kb DNA molecularweight ladder and E. coli gDNA samples subjected to increasing amountsof 4.67 M tetramethyl ammonium acetate as DNA bind modifier during thebinding reaction using borosilicate glass spin filters. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 35 μL.

FIG. 15A shows the electrophoretic separation of PCR reactions generatedusing appropriate primers.

FIG. 15B compares the electrophoretic separation of 1 kb DNA molecularweight ladder and PCR product samples subjected to increasing amounts of4.7 M tetramethyl ammonium acetate as DNA bind modifier during thebinding reaction using borosilicate glass spin filters. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 25 μL.

FIG. 16 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the initial binding reaction using borosilicate glass spinfilters further subjected to a secondary bind. Different volumes ofethanol were used as secondary bind. Samples in lanes 1 and 2 containedthe 1 kb DNA molecular weight ladder sample in the absence of any DNAbind modifiers. Samples in lanes 3-10 contained 35 μL of 4.7 Mtetramethyl ammonium acetate used as DNA bind modifier in the initialbind. Samples in lanes 5-10 were the recovered flow through of 1 kb DNAmolecular weight ladder passed through a borosilicate glass spin filterin the presence of 35 μL of 4.7 M tetramethyl ammonium acetate subjectedto a secondary bind using different volumes of neat ethanol.

FIG. 17 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of increasing amounts of 4.67 Mtetramethyl ammonium acetate as DNA bind modifiers using borosilicateglass spin filters with a simultaneous selection strategy and a stepwiseselection strategy. DNA bind modifier was added to the DNA sample priorto loading on the spin filter for simultaneous selection and added tothe spin filter bound with DNA for stepwise selection (on-filterselection). In this gel, DNA bind modifier volumes were varied from 0 to35 μL.

FIG. 18 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of different amounts of 4.67 Mtetramethyl ammonium acetate as DNA bind modifier using borosilicateglass spin filters in a stepwise binding method. Sample A was 1 kb DNAmolecular weight ladder subjected to 4.7 M tetramethyl ammonium acetateduring an initial binding reaction using borosilicate glass spinfilters. Sample B was 1 kb DNA molecular weight ladder subjected to 4.7M tetramethyl ammonium acetate during an initial binding reaction usingborosilicate glass spin filters subjected to a secondary bindingreaction using the same DNA bind modifier. Sample C was the recoveredflow through of Sample A. Sample D was the recovered flow through ofSample B. In this gel, the nucleic acid binding solution was heldconstant at 170 L while DNA bind modifier volumes were varied from 25 to35 μL.

FIG. 19 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the initial binding reaction using borosilicate glass spinfilters and further subjected to a secondary bind. Differentconcentrations of ethanol were used as secondary bind. Samples in lanes1 and 2 contained the 1 kb DNA molecular weight ladder sample in theabsence of any DNA bind modifiers. Samples in lanes 3-12 contained 35 μL4.7 M tetramethyl ammonium acetate used as DNA bind modifier in theinitial bind. Samples in lanes 5-12 were the recovered flow through of 1kb DNA molecular weight ladder passed through a borosilicate glass spinfilter in the presence of 35 μL of 4.7 M tetramethyl ammonium acetatesubjected to a second bind using different concentrations of ethanol.

FIG. 20A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifier(4.67 M tetramethyl ammonium acetate) during the initial bindingreaction using borosilicate glass spin filters and further subjected toa secondary bind. During the secondary bind, the flow through was notmixed with other solutions, mixed with ethanol, or with mixed withwater.

FIG. 20B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifier(4.67 M tetramethyl ammonium acetate) during the initial bindingreaction using borosilicate glass spin filters and further subjected toa secondary bind. During the secondary bind, the flow through wasdiluted with 1 volume of water, 2 volumes of water, 3 volumes of wateror 1 volume of EtOH.

FIG. 21A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding solutions with differentguanidine HCl concentrations during the binding reaction usingborosilicate glass spin filters. Nucleic acid binding buffers with 1.5M, 2 M, and 3 M guanidine HCl were used. In this gel, the differentnucleic acid binding solutions was held constant at 170 μL and DNAsample was held constant at 50 μL.

FIG. 21B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding solutions with differentguanidine HCl concentrations during the binding reaction usingborosilicate glass spin filters. Nucleic acid binding buffers with 0.375M, 0.75 M, and 1.5 M guanidine HCl were used. In this gel, the differentnucleic acid binding solutions was held constant at 170 μL and DNAsample was held constant at 50 μL.

FIG. 22A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different concentrations of DNA bindmodifier during the binding reaction using borosilicate glass spinfilters. Increasing amounts of 4.7 M and 3.8 M tetramethyl ammoniumacetate were used as DNA bind modifiers. In this gel, the nucleic acidbinding solution was held constant at 170 μL while DNA bind modifiervolumes were varied from 0 to 35 μL.

FIG. 22B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier during the binding reaction using borosilicate glass spinfilters. 3 M tetramethyl ammonium acetate was used as DNA bind modifier.In this gel, the nucleic acid binding solution was held constant at 170μL while DNA bind modifier volumes were varied from 0 to 35 μL.

FIG. 23 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding solutions with differentguanidine HCl concentrations in the presence or absence of increasingamounts of DNA bind modifier (4.67 M tetramethyl ammonium acetate)during the binding reaction using borosilicate glass spin filters. DNAbinding solutions with 1.5 M and 3 M guanidine HCl were used. In thisgel, the different DNA binding solutions was held constant at 170 μL andDNA sample was held constant at 50 μL.

FIG. 24A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof DNA binding solution and DAP amount was kept constant at 35 μL (DAPdilutions were varied from 1 to 100%).

FIG. 24B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof nucleic acid binding solution and DAP amount was kept constant at 35μL (DAP dilutions were varied from 30 to 50%).

FIG. 24C compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof DNA binding solution and DAP amount was kept constant at 35 μL (DAPdilutions were varied from 25 to 100%).

FIG. 25 compares electrophoretic separation of 1 kb DNA molecular weightladder samples contacted with silica-coated magnetic beads (SwiftMag®beads) in the presence or absence of DNA bind modifier. Differentamounts of 4.7 M tetramethyl ammonium acetate and 2.02 M diammoniumphosphate (DAP) were used as DNA bind modifier. 50 μL of DNA ladder wascombined with 170 μL DNA Binding Solution and 0-35 μL of DNA bindmodifier.

FIG. 26 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifierduring the binding reaction using borosilicate glass spin filters withor without pretreatment with the DNA bind modifier. 4.7 M tetramethylammonium acetate and 2.02 M diammonium phosphate (DAP) were used as DNAbind modifiers. Sample A was a control sample that did not contain DNAbind modifier. 50 μL of DNA ladder was combined with 170 μL of DNAbinding solution and 35 μL of DNA bind modifier in Samples B and C. InSamples D and E, a mixture of 50 μL of DNA ladder, 170 μL of DNA bindingsolution, and 35 μL of the indicated DNA bind modifier was subjected toa spin filter pretreated with 35 μL of the same DNA bind modifier and170 μL DNA binding solution. In Samples F and G, a mixture of 50 μL ofDNA ladder, 170 μL of DNA binding solution, and 35 μL of the indicatedDNA bind modifier was subjected to a spin filter pretreated with 170 ofthe same DNA bind modifier.

DETAILED DESCRIPTION

A detailed description of one or more embodiments of the claimed subjectmatter is provided below along with accompanying figures that illustratethe principles of the claimed subject matter. The claimed subject matteris described in connection with such embodiments, but is not limited toany particular embodiment. It is to be understood that the claimedsubject matter may be embodied in various forms, and encompassesnumerous alternatives, modifications and equivalents. Therefore,specific details disclosed herein are not to be interpreted as limiting,but rather as a basis for the claims and as a representative basis forteaching one skilled in the art to employ the claimed subject matter invirtually any appropriately detailed system, structure, or manner.Numerous specific details are set forth in the following description inorder to provide a thorough understanding of the present disclosure.These details are provided for the purpose of example and the claimedsubject matter may be practiced according to the claims without some orall of these specific details. It is to be understood that otherembodiments can be used and structural changes can be made withoutdeparting from the scope of the claimed subject matter. It should beunderstood that the various features and functionality described in oneor more of the individual embodiments are not limited in theirapplicability to the particular embodiment with which they aredescribed. They instead can, be applied, alone or in some combination,to one or more of the other embodiments of the disclosure, whether ornot such embodiments are described, and whether or not such features arepresented as being a part of a described embodiment. For the purpose ofclarity, technical material that is known in the technical fieldsrelated to the claimed subject matter has not been described in detailso that the claimed subject matter is not unnecessarily obscured.

All publications, including patent documents, scientific articles anddatabases, referred to in this application are incorporated by referencein their entireties for all purposes to the same extent as if eachindividual publication were individually incorporated by reference. If adefinition set forth herein is contrary to or otherwise inconsistentwith a definition set forth in the patents, patent applications,published applications or other publications that are hereinincorporated by reference, the definition set forth herein prevails overthe definition that is incorporated herein by reference. Citation of thepublications or documents is not intended as an admission that any ofthem is pertinent prior art, nor does it constitute any admission as tothe contents or date of these publications or documents.

All headings are for the convenience of the reader and should not beused to limit the meaning of the text that follows the heading, unlessso specified.

The practice of the provided embodiments will employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and sequencing technology,which are within the skill of those who practice in the art. Suchconventional techniques include polypeptide and protein synthesis andmodification, polynucleotide synthesis and modification, polymer arraysynthesis, hybridization and ligation of polynucleotides, and detectionof hybridization using a label. Specific illustrations of suitabletechniques can be had by reference to the examples herein. However,other equivalent conventional procedures can, of course, also be used.Such conventional techniques and descriptions can be found in standardlaboratory manuals such as Green, et al., Eds., Genome Analysis: ALaboratory Manual Series (Vols. I-IV) (1999); Weiner, Gabriel, Stephens,Eds., Genetic Variation: A Laboratory Manual (2007); Dieffenbach,Dveksler, Eds., PCR Primer: A Laboratory Manual (2003); Bowtell andSambrook, DNA Microarrays: A Molecular Cloning Manual (2003); Sambrookand Russell, Condensed Protocols from Molecular Cloning: A LaboratoryManual (2006); and Sambrook and Russell, Molecular Cloning: A LaboratoryManual (2002) (all from Cold Spring Harbor Laboratory Press); Gait,Oligonucleotide Synthesis: A Practical Approach (2002), IRL Press,London; Nelson and Cox, Lehninger, Principles of Biochemistry (2000) 3rdEd., W. H. Freeman Pub., New York, N.Y., all of which are hereinincorporated in their entireties by reference for all purposes.

In one aspect, provided herein are methods and compositions for thesize-selective isolation of nucleic acid molecules (e.g., DNA or RNA)from a nucleic acid-containing sample (e.g., a biological sample). Inanother aspect, provided herein are methods and compositions forisolating nucleic acid molecules of a target size range from a nucleicacid-containing sample. This technique is useful, for example, in thepreparation of next generation sequencing libraries as it allows verylarge barcoded and/or ligated PCR primers and any unintended PCR sideproducts to be removed from the reaction mix prior to the sequencingreactions.

The methods and compositions provided herein can be used for negativelyand/or positively selecting for nucleic acid molecules in a particularsize range. In some embodiments, the target nucleic acid molecules havea size range with a lower size limit. For example, the target nucleicacid molecules are more than about 1 kb in length (i.e., 1000 basepair). In some embodiments, the target nucleic acid molecules have asize range with an upper size limit. For example, the target nucleicacid molecules are less than about 5 kb in length. In some embodiments,the target nucleic acid molecules have a size range with both a lowersize limit and an upper size limit. For example, the target nucleic acidmolecules are between about 1 kb and about 5 kb in length.

In some aspects, provided herein are methods and compositions for sizeselection via small-molecule modulation of nucleic acid binding to aborosilicate or a silica surface. In one aspect, in the absence of thesmall-molecule modulator, all nucleic acid sizes bind. When thesmall-molecule modulator is introduced, nucleic acid binding is reducedin a size-dependent fashion, giving this process a great deal ofsynthetic control. In some aspects, the small-molecule modulator is acarboxylate molecule, for example, a carboxylate anion. In one aspect,in the absence of the exogenous carboxylate anion, all nucleic acidsizes bind. When carboxylate anion is introduced, nucleic acid bindingis reduced in a size-dependent fashion, giving this process a great dealof synthetic control.

In some aspects, the small-molecule modulator is a cation. For instance,a small-molecule modulator may contain a positively charged functionalgroup that can participate in electrostatic interactions with thephosphodiester backbone of DNA and/or RNA. Cations include, withoutlimitation, ammonium and substituted ammonium cations, such as ammonium,tetramethylammonium, choline (N,N,N-tetramethylethanolammonium), andtris(2-hydroxyethyl)methylammonium. Cations provided herein may furthercontain or be associated with any appropriate anion, including, withoutlimitation, acetate, phosphate, chloride, sulfate, methylsulfate, orsilicate. Particular small-molecule modulators include ammonium acetate,ammonium chloride, tetramethylammonium acetate, tetramethylammoniumacetate tetrahydrate, ammonium phosphate dibasic, choline chloride,tris(2-hydroxyethyl)methylammonium methylsulfate (TMAMS),tetramethylammonium silicate, and ammonium sulfate.

In another aspect, the small-molecule modulator is an oxyanion. Forinstance, the oxyanion may be able to directly compete with nucleic acidphosphates for binding sites on the silica resin. Oxyanions includephosphates, phosphonates, and borates. Oxyanions may have one or moresites of deprotonation, such as one, two, or three sites ofdeprotonation. Oxyanions provided herein may further contain or beassociated with any appropriate cation. Particular small-moleculemodulators include monopotassium phosphate, dipotassium phosphate,tripotassium phosphate, monosodium phosphate, disodium phosphate,trisodium phosphate, 3-aminopropylphosphonic acid, and(aminomethyl)phosphonic acid.

In another aspect, the small-molecule modulator is a compound containingboth a cation and an oxyanion covalently attached to one another. Thecompound may contain any cation provided herein and any oxyanionprovided herein, which are covalently attached to one another.Particular small-molecule modulators are compounds that contain both acarboxylate, phosphate, phosphonate, or borate moiety covalentlyattached to an ammonium or substituted ammonium moiety.

Provided in some embodiments is a method of isolating nucleic acidmolecules from a sample according to molecular weight. In someembodiments, the nucleic acid molecules originate from a biologicalsample. In some embodiments, the nucleic acids have been processed, forexample, the nucleic acids have been amplified using a method such asPCR. Nucleic acids isolated using the methods and kits provided hereinmay be used in the areas of molecular biological application, including,for example, analytical, cloning, diagnostic, and detection. In someembodiments, the isolated nucleic acids are used as part of a sequencinglibrary for next generation sequencing.

In some embodiments, the nucleic acid sample to be isolated comprisesDNA. In some embodiments, the nucleic acid sample comprises RNA. In someembodiments, the nucleic acid sample to be isolated comprises DNA andRNA. In some embodiments, the nucleic acid (e.g., DNA or RNA) is in anynaturally occurring modification thereof, or combinations thereof. Insome aspects, the nucleic acid is genomic DNA and may be in a single ordouble stranded or in any other form.

Provided in some embodiments is a method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample. In someembodiments, the target nucleic acid molecules are within a particularmolecular size range and non-target nucleic acid molecules are outsidethe molecular size range. In some embodiments, the sample comprisingnucleic acid molecules are placed in contact with a matrix in thepresence of a carboxylate compound. In some embodiments, the targetnucleic acid molecules selectively bind to the matrix and the non-targetnucleic acid molecules do not bind to the matrix. In some embodiments,the method further comprises a step wherein the matrix is washed toremove the unbound nucleic acid. In some embodiments, the method furthercomprises a step wherein the bound target nucleic acid molecules can becollected by eluting the bound nucleic acid molecules from the matrix.

In some embodiments, the target nucleic acid molecules are of aparticular molecular size range. In some embodiments, the target nucleicacid molecules are greater than a particular size cut-off. In someembodiments, the target nucleic acid molecules are greater than about100-5000 bp, such as greater than about 5000 bp, greater than about 4000bp, greater than about 3000 bp, greater than about 2000 bp, greater thanabout 1500 bp, greater than about 1000 bp, greater than about 600 bp,greater than about 400 bp, or greater than about 200 bp.

It is to be understood that while the terms “target nucleic acidmolecules” and “non-target nucleic acid molecules” are used herein forthe purpose of illustration, the non-target nucleic acid moleculesisolated from the target nucleic acid molecules can nonetheless beuseful for a downstream application.

In some embodiments, a sample containing the nucleic acid molecules iscontacted with a matrix in the presence of a carboxylate compound. Insome embodiments, the matrix comprises silica. In some embodiments, thematrix comprises borosilicate glass. In some embodiments, the matrixcomprises silicon dioxide. In some embodiments, the matrix comprisessilicon dioxide-coated magnetic beads. In some embodiments, the matrixcomprises SwiftMag® beads. In some embodiments, the matrix comprises ametal oxide. Exemplary metal oxides are iron oxide and magnesium oxide.

In some embodiments, the carboxylate compound is in a solution. In someembodiments, the carboxylate is soluble in water at concentrations of upto 32 M. In some embodiments, the carboxylate is soluble in water atconcentrations of up to 16 M. In some embodiments, the carboxylate issoluble in water at concentrations of up to 8 M (e.g., up to 6 M, up to4 M, up to 2 M, or up to 1 M). In some embodiments, the R group of thecarboxylate cannot be ionized to a negative species within the range ofpH 4-9 (e.g., pH 4-6, 5-7, 6-8, or 7-9).

In some embodiments, the small-molecule modulator is attached to thematrix. In some embodiments, the carboxylate compound is attached to thematrix.

In some embodiments, the carboxylate compound is of the formula (I):

wherein R¹ is a structural moiety that satisfies the following twoconditions: 1) R¹ does not render the carboxylate insoluble in water athigh concentration (preferably 1-8 M); and 2) R¹ cannot be ionized to anegative species within the range of pH 4-9; M is a metal or N(R^(a))₄;each R^(a) is independently H or alkyl; and n is 1, 2, or 3; or ahydrate thereof.

In some embodiments, the carboxylate compound is of the formula (I):

wherein R² is a phosphate or a phosphonic acid (e.g., phosphonoaceticacid); M is a metal or N(R^(a))₄; each R^(a) is independently H oralkyl; and n is 1, 2, or 3; or a hydrate thereof.

In some embodiments, the carboxylate compound is of the formula (I):

wherein

-   -   R is selected from the group consisting of H, substituted or        unsubstituted C₁-C₈ alkyl, substituted or unsubstituted C₁-C₈        alkenyl, and substituted or unsubstituted C₁-C₈ alkynyl;    -   M is a metal or N(R^(a))₄;    -   each R^(a) is independently H or alkyl; and    -   n is 1, 2, or 3;    -   or a hydrate thereof.

In some embodiments, R is H. In some embodiments, R is unsubstitutedC₁-C₈ alkyl. In some embodiments, R is CH₃. In some embodiments, R is asubstituted C₁-C₈ alkyl. In some embodiments, R is C₁-C₈ alkylsubstituted with one or more halogen. In some embodiments, R is C₁-C₈perhaloalkyl, such as trifluoromethyl or trichloromethyl. In someembodiments, R is substituted or unsubstituted C₁-C₈ alkenyl. In someembodiments, R is substituted or unsubstituted C₁-C₈ alkynyl.

In some embodiments, the compound of any of formula (Ia), (Ib), or (I)is soluble in water at concentrations of up to 8 M (e.g., up to 6 M, upto 4 M, up to 2 M, or up to 1 M). In some embodiments, the R group ofthe compound of formula (I) cannot be ionized to a negative specieswithin the range of pH 4-9 (e.g., pH 4-6, 5-7, 6-8, or 7-9).

In some embodiments of any of formulae (Ia), (Ib), and (I), M is analkali metal such as Li, Na or K. In some embodiments, M is an alkalineearth metal such as Ca or Mg. In other embodiments, M is a metalloidsuch as Al. In some embodiments, M is N(R^(a))₄. In some suchembodiments, one R^(a) group is alkyl (e.g., methyl or ethyl), and theother R^(a) groups are H. In some such embodiments, two R^(a) groups areindependently alkyl (e.g., methyl or ethyl), and the other R^(a) groupsare H. In some such embodiments, three R^(a) groups are independentlyalkyl (e.g., methyl or ethyl), and the other R^(a) group is H. In somesuch embodiments, all four R^(a) groups are independently alkyl (e.g.,methyl or ethyl). In some embodiments, M is NH₄. In some embodiments,M^(n+) is a monovalent cation, such that n=1. In other embodiments,M^(n+) is a multivalent cation, such that n=2 or 3. In some embodiments,M^(n+) is Na⁺, Li⁺, K⁺, Ca²⁺, Mg²⁺, Al³⁺, or NH₄ ⁺.

In some embodiments, the sample comprising nucleic acid molecules isplaced in contact with the small-molecule modulators prior to contactwith the matrix. In some embodiments, the sample comprising nucleic acidmolecules is placed in contact with the matrix prior to contact with thesmall-molecule modulators. In some embodiments, the small-moleculemodulators are contacted with the matrix prior to contact with thesample comprising the nucleic acid molecules. In other embodiments, thesample containing the nucleic acid molecules is simultaneously contactedwith the small-molecule modulators and the matrix.

In some embodiments, the concentration of the small-molecule modulatoraffects the binding selectivity of the target nucleic acid molecules tothe matrix. In some embodiments, the small-molecule modulator is presentin sufficient concentration that the target nucleic acid moleculesselectively bind to the matrix. In some embodiments, the non-targetnucleic acid molecules do not bind to the matrix. In some embodiments,nucleic acid molecules having a size above a certain molecular weightrange bind to the matrix while nucleic acid molecules having a sizebelow that molecular weight range do not bind to the matrix. In someembodiments, increasing the concentration of the small-moleculemodulator increases the molecular weight cut-off for nucleic acidmolecules that bind to the matrix.

In some embodiments, the small-molecule modulator is in a solution. Insome embodiments, the small-molecule modulator can be added to a nucleicacid binding solution. In some embodiments, the nucleic acid bindingsolution may further comprise one or more additional components, such asa buffering agent, a chelating agent, a salt, or an additional solvent.Examples of buffering agents include, but are not limited to, Tris, PBS,MOPS, MES, and HEPES. Examples of chelating agent include, but are notlimited to, EDTA, EGTA, DTPA, and BAPTA. Examples of salts include, butare not limited to guanidine hydrochloride, Tris-HCl, NaCl, NH₄Cl,MgCl₂, KH₂PO₄, and K₂HPO₄. Further examples of salts include guanidinecarbonate, guanidine phosphate, guanidine sulfate, and guanidinethiocyanate. Examples of additional solvents include, but are notlimited to, water-miscible protic or aprotic solvents of the appropriatedielectric constant such as ketones (e.g., acetone), alcohols (e.g.,methanol, ethanol, isopropanol, and butanol) and dimethylsulfoxide. Insome embodiments, the nucleic acid binding solution comprises guanidinehydrochloride, Tris-HCl, and isopropanol. In some embodiments, thesmall-molecule modulator is present in a sufficient concentration topromote binding of the nucleic acid molecules to the matrix. In someembodiments, the small-molecule modulator is in a concentration in therange of about 0.01 M to about 8 M, such as about 0.05 M to about 7 M,about 0.1 M to about 6 M, about 0.2 M to about 5 M, about 0.5 M to about4 M, about 0.75 M to about 3 M, and about 1 M to about 2 M. In someembodiments the small-molecule modulator is in a concentration belowabout 32 M, such as below about 16 M, below about 8 M, below about 6 M,below about 4 M, below about 2 M, or below about 1 M. In someembodiments the small-molecule modulator is in a concentration aboveabout 32 M, such as above about 16 M, above about 8 M, above about 6 M,above about 4 M, above about 2 M, above about 1 M, above about 0.5 M, orabove about 0.1 M.

In some embodiments, the carboxylate compound is selected from the groupconsisting of ammonium acetate, sodium acetate, sodium formate, sodiumpropanoate, sodium trimethylacetate hydrate, sodium trichloroacetate,and sodium trifluoroacetate. In some embodiments, a combination of thevarious carboxylate compounds disclosed herein is used. In someembodiments, a combination of the various small-molecule modulatorsdisclosed herein is used.

In some embodiments, the sample comprising nucleic acid molecules isplaced in contact with the carboxylate compounds prior to contact withthe matrix. In some embodiments, the sample comprising nucleic acidmolecules is placed in contact with the matrix prior to contact with thecarboxylate compounds. In some embodiments, the carboxylate compoundsare contacted with the matrix prior to contact with the samplecomprising the nucleic acid molecules. In other embodiments, the samplecontaining the nucleic acid molecules is simultaneously contacted withthe carboxylate compounds and the matrix.

In some embodiments, the concentration of the carboxylate compoundaffects the binding selectivity of the target nucleic acid molecules tothe matrix. In some embodiments, the carboxylate compound is present insufficient concentration that the target nucleic acid moleculesselectively bind to the matrix. In some embodiments, the non-targetnucleic acid molecules do not bind to the matrix. In some embodiments,nucleic acid molecules having a size above a certain molecular weightrange bind to the matrix while nucleic acid molecules having a sizebelow that molecular weight range do not bind to the matrix. In someembodiments, increasing the concentration of the carboxylate compoundincreases the molecular weight cut-off for nucleic acid molecules thatbind to the matrix.

In some embodiments, the carboxylate compound is in a solution. In someembodiments, the carboxylate compound can be added to a nucleic acidbinding solution. In some embodiments, the nucleic acid binding solutionmay further comprise one or more additional components, such as abuffering agent, a chelating agent, a salt, or an additional solvent.Examples of buffering agents include, but are not limited to, Tris, PBS,MOPS, MES, and HEPES. Examples of chelating agent include, but are notlimited to, EDTA, EGTA, DTPA, and BAPTA. Examples of salts include, butare not limited to guanidine hydrochloride, Tris-HCl, NaCl, NH₄Cl,MgCl₂, KH₂PO₄, and K₂HPO₄. Further examples of salts include guanidinecarbonate, guanidine phosphate, guanidine sulfate, and guanidinethiocyanate. Examples of additional solvents include, but are notlimited to, water-miscible protic or aprotic solvents of the appropriatedielectric constant such as ketones (e.g., acetone), alcohols (e.g.,methanol, ethanol, isopropanol, and butanol) and dimethylsulfoxide. Insome embodiments, the nucleic acid binding solution comprises guanidinehydrochloride, Tris-HCl, and isopropanol. In some embodiments, thecarboxylate compound is present in a sufficient concentration to promotebinding of the nucleic acid molecules to the matrix. In someembodiments, the carboxylate compound is in a concentration in the rangeof about 0.01 M to about 8 M, such as about 0.05 M to about 7 M, about0.1 M to about 6 M, about 0.2 M to about 5 M, about 0.5 M to about 4 M,about 0.75 M to about 3 M, and about 1 M to about 2 M. In someembodiments the carboxylate compound is in a concentration below about32 M, such as below about 16 M, below about 8 M, below about 6 M, belowabout 4 M, below about 2 M, or below about 1 M. In some embodiments thecarboxylate compound is in a concentration above about 32 M, such asabove about 16 M, above about 8 M, above about 6 M, above about 4 M,above about 2 M, above about 1 M, above about 0.5 M, or above about 0.1M.

In some embodiments, the matrix is washed to remove the unbound nucleicacid molecules. In some embodiments, the matrix is washed using a washbuffer. In some embodiments, the wash buffer is an aqueous solution thatmay comprise one or more components, such as a buffering agent, achelating agent, a salt, or an additional solvent. Examples of bufferingagents include, but are not limited to, Tris, PBS, MOPS, MES, and HEPES.Examples of chelating agent include, but are not limited to, EDTA, EGTA,DTPA, and BAPTA. Examples of salts include, but are not limited to NaCl,NH₄Cl, MgCl₂, KH₂PO₄, and K₂HPO₄. Examples of additional solventsinclude, but are not limited, water-miscible protic or aprotic solventsof the appropriate dielectric constant such as ketones (e.g., acetone),alcohols (e.g., methanol, ethanol, isopropanol, and butanol) anddimethylsulfoxide. In some embodiments, the wash buffer comprises one ormore of Tris, EDTA, NaCl, and ethanol. In some embodiments, the washbuffer has a pH of between about 7 and about 8, such as between about pH7.4-7.9.

In some embodiments, the nucleic acid molecules bound to the matrix areeluted from the matrix using an eluent. In some embodiments, the nucleicacid molecules bound to the matrix are eluted with PCR-grade water. Insome embodiments, the nucleic acid molecules bound to the matrix areeluted with a buffering agent, such as Tris, PBS, MOPS, MES, HEPES, orany combination thereof. In other embodiments, the nucleic acidmolecules bound to the matrix are eluted withTris(hydroxymethyl)aminomethane (Tris) solution. In some embodiments,the pH of the eluent is between about 7-9, such as about 8.

In some embodiments, any of the methods described herein are performedin the absence of polyethylene glycol (PEG).

In some embodiments, the method provides conditions that inhibit thebinding of non-target nucleic acid molecules to the matrix, wherein thenon-target nucleic acid molecules are below a certain molecular weightcut-off value. In some embodiments, nucleic acid molecules having a sizeabove a certain cut-off value bind to the matrix while nucleic acidmolecules having a size below a certain cut-off value do not bind to thematrix. In some embodiments, the cut-off value lies in the range ofabout 5000-12000 bp, such as about 8000-12000 bp, about 6000-9000 bp, orabout 5000-7000 bp. In some embodiments, the cut-off value lies in therange of about 2000-6000 bp, such as about 4000-6000 bp, about 3000-5000bp, or about 2000-4000 bp. In some embodiments, the cut-off value liesin the range of about 500-3000 bp, such as about 1500-3000 bp, 1000-2000bp, or 500-1000 bp. In some embodiments, the cut-off value lies in therange of about 100-1000 bp, such as between about 700-1000 bp, betweenabout 500-800 bp, between about 300-600 bp, or between about 100-400 bp.In some embodiments, the cut-off value is about 12,000 bp, about 10,000bp, about 7,000 bp, about 5,000 bp, about 3,000 bp, about 2,000 bp,about 1,500 bp, about 1,000 bp, about 850 bp, about 650 bp, about 500bp, about 400 bp, about 300 bp, about 200 bp, or about 100 bp.

In some embodiments, the target nucleic acid molecules are within aparticular molecular weight range and the non-target nucleic acidmolecules are outside the molecular weight range. In some embodiments,greater than about 99% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 95% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 90% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 80% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 70% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 60% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules. In some embodiments,greater than about 50% wt. % of the nucleic acid molecules that bind tothe matrix are the target nucleic acid molecules.

In some embodiments, greater than about 99% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 95% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 90% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 80% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 70% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 60% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.In some embodiments, greater than about 50% of the nucleic acidmolecules that bind to the matrix are the target nucleic acid molecules.

In some embodiments, the nucleic acid molecules that bind to the matrixare utilized in further processes or analytical methods. In someembodiments, the nucleic acid molecules that do not bind to the matrixare utilized in further processes or analytical methods. In someembodiments, nucleic acid molecules above a certain molecular weightrange can be obtained by collecting the nucleic acid molecules that arebound to the matrix. In some embodiments, nucleic acid molecules below acertain molecular weight can be obtained by collecting the nucleic acidmolecules that are not bound to the matrix (i.e., that are eluted fromthe matrix).

In other embodiments, nucleic acid molecules within a particularmolecular size range, e.g., nucleic acid molecules that have molecularweight of intermediate value, can be obtained by using a double-sidedselection method. In some embodiments, the double sided selection methodcomprises two or more steps. In some embodiments, the double-sidedselection method requires the use of two or more separate matrices. Insome embodiments, the two or more matrices used in the double-sidedselection method have the same composition. In some embodiments, the twoor more matrices used in the double-sided selection method are differentin composition. In some embodiments, the double-sided selection methodcomprises a first step of removing the larger nucleic acid molecules(i.e., nucleic acid molecules that are above the desired size range) bycontacting the nucleic acid-containing sample with a first matrix in thepresence of a first carboxylate compound in a concentration that issufficient for selectively binding the larger nucleic acid molecules tothe first matrix. In some embodiments, the doubled-sided selectionmethod comprises washing the first matrix to collect the unbound nucleicacid molecules for further processing. In some embodiments, the firstmatrix with the bound nucleic acid molecules from the first step isdiscarded. In some embodiments, the double-sided selection methodcomprises a further step of removing the smaller nucleic acid molecules(i.e., nucleic acid molecules that are below the desired size range),wherein the unbound nucleic acid molecules from the first step arecontacted with a second matrix in the presence of a second carboxylatecompound in a concentration that is sufficient to selectively removesmaller nucleic acid molecules that are not bound to the second matrix.In some embodiments, the second matrix is washed to remove the unboundnucleic acid molecules. In some embodiments, the second matrix is elutedto obtain the nucleic acid molecules within the desired size range(e.g., that are intermediate in size).

In some embodiments, the double-sided selection method comprises a firststep of removing smaller nucleic acid molecules (i.e., nucleic acidmolecules that are below the desired size range) by contacting thenucleic acid-containing sample with a first matrix in the presence of afirst carboxylate compound in a concentration that is sufficient forselectively binding larger nucleic acid molecules. In some embodiments,the doubled-sided selection method comprises washing the first matrix toremove the unbound smaller nucleic acid molecules from the first matrix.In some embodiments, the first matrix with the bound larger nucleic acidmolecules is contacted with a second carboxylate compound of a differentconcentration such that nucleic acid molecules that are above thedesired size range remain bound to the first matrix while nucleic acidsof the desired size range are washed from the matrix. In otherembodiments, the first matrix with the bound nucleic acid molecules fromthe first step is eluted, and the eluted nucleic acid molecules arefurther processed. In some embodiments, the double-sided selectionmethod comprises a further step of removing the larger nucleic acidmolecules (i.e., nucleic acid molecules that are above the desired sizerange), wherein the eluted nucleic acid molecules from the first stepare contacted with a second matrix in the presence of a secondcarboxylate compound in a concentration that is sufficient toselectively bind the larger nucleic acid molecules (i.e., nucleic acidmolecules that are above the desired size range) that are still present.In some embodiments, the unbound nucleic acid molecules are collected.In some embodiments, the second matrix is washed to obtain the unboundnucleic acid molecules. In some embodiments, the unbound nucleicmolecules are within the desired size range (e.g., are intermediate insize).

In some embodiments, the concentration of small-molecule modulator usedin the first step is greater than the concentration of small-moleculemodulator used in the second step. In some embodiments, theconcentration of small-molecule modulator used in the first step is lessthan the concentration of small-molecule modulator used in the secondstep. In some embodiments, the concentration of small-molecule modulatorused in each step of the double-sided selection method can be adjustedto obtain nucleic acid molecules between a certain molecular range,wherein the molecular range has a lower molecular weight cut-off limitand a higher molecular weight cut-off limit.

In some embodiments, the concentration of carboxylate compound used inthe first step is greater than the concentration of carboxylate compoundused in the second step. In some embodiments, the concentration ofcarboxylate compound used in the first step is less than theconcentration of carboxylate compound used in the second step. In someembodiments, the concentration of carboxylate compound used in each stepof the double-sided selection method can be adjusted to obtain nucleicacid molecules between a certain molecular range, wherein the molecularrange has a lower molecular weight cut-off limit and a higher molecularweight cut-off limit.

Provided herein are kits comprising a small-molecule modulator, amatrix, and instructions describing a method for use according to any ofthe embodiments described herein. Also provided herein are kitscomprising a carboxylate compound, a matrix, and instructions describinga method for use according to any of the embodiments described herein.In some embodiments, the kit may contain any of the compositions orcombinations described herein. In some embodiments, the kit contains thecompositions or combinations in a concentrated form. In someembodiments, the kit contains the compositions or combinations in solidform. In some embodiments, the kit contains the compositions orcombinations in solution form. In some embodiments, the kit additionallycontains solutions for dissolving or diluting the compositions andcombinations prior to use. In some embodiments, the kit may additionallycomprise solutions such as nucleic acid binding solutions, wash buffers,or elution solutions. Selected compositions including articles ofmanufacture thereof can also be provided as kits. Exemplary articles ofmanufacture include containers such as vials, bottles, jars, cans, andtubes.

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural referents unless the context clearly dictatesotherwise. For example, “a” or “an” means “at least one” or “one ormore.” Thus, reference to “a carboxylate compound” refers to one or morecarboxylate compounds, and reference to “the method” includes referenceto equivalent steps and methods disclosed herein and/or known to thoseskilled in the art, and so forth. It is understood that aspects andvariations described herein include “consisting” and/or “consistingessentially of” aspects and variations.

Throughout this disclosure, various aspects of the claimed subjectmatter are presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theclaimed subject matter. Accordingly, the description of a range shouldbe considered to have specifically disclosed all the possible sub-rangesas well as individual numerical values within that range. For example,where a range of values is provided, it is understood that eachintervening value, between the upper and lower limit of that range andany other stated or intervening value in that stated range isencompassed within the claimed subject matter. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges, and are also encompassed within the claimed subjectmatter, subject to any specifically excluded limit in the stated range.Where the stated range includes one or both of the limits, rangesexcluding either or both of those included limits are also included inthe claimed subject matter. This applies regardless of the breadth ofthe range.

The term “about” as used herein refers to the usual error range for therespective value readily known to the skilled person in this technicalfield. Reference to “about” a value or parameter herein includes (anddescribes) embodiments that are directed to that value or parameter perse. For example, description referring to “about X” includes descriptionof “X”.

The term “alkyl” refers to saturated aliphatic groups includingstraight-chain, branched-chain, and cyclic groups having from 1 to 12carbon atoms. “C_(x)-C_(y) alkyl” refers to alkyl groups with x to ycarbon atoms. For example, “C₁-C₈ alkyl” refers to alkyl groups with 1to 8 carbon atoms in the chain. Examples of alkyl groups include, butare not limited to, methyl (Me), ethyl (Et), n-propyl, isopropyl, butyl,isobutyl, sec-butyl, tert-butyl (tBu), pentyl, isopentyl, tert-pentyl,hexyl, and isohexyl.

The term “alkenyl” refers to unsaturated aliphatic groups includingstraight-chain, branched-chain, and cyclic groups having from 2 to 12carbon atoms and at least one double bond. “C_(x)-C_(y) alkenyl” refersto alkenyl groups with x to y carbon atoms. For example, “C₂-C₈ alkenyl”refers to alkenyl groups with 2 to 8 carbon atoms in the chain. Examplesof alkenyl groups include, but are not limited to, ethenyl, 2-propenyl,2-methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl,2-methyl-1-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl.

The term “alkynyl” refers to unsaturated aliphatic groups includingstraight-chain, branched-chain, and cyclic groups having from 2 to 12carbon atoms and at least one triple bond. “C_(x)-C_(y) alkynyl” refersto alkynyl groups with x to y carbon atoms. For example, “C₂-C₈ alkynyl”refers to alkynyl groups with 2 to 8 carbon atoms in the chain. Examplesof alkynyl groups include, but are not limited to, ethynyl, 1-propynyl,1-butynyl, 2-butynyl, and 1-methyl-2-butynyl.

The term “substituted” means that the specified group or moiety bearsone or more substituents. The term “unsubstituted” means that thespecified group bears no substituents. The term “optionally substituted”means that the specified group is unsubstituted or substituted by one ormore substituents. Where the term “substituted” is used to describe astructural system, the substitution is meant to occur at anyvalency-allowed position on the system.

As used herein, the term “binding” and cognates thereof refers to anattractive interaction between two molecules which results in a stableassociation in which the molecules are in close proximity to each other.Molecular binding can be classified into the following types:non-covalent, reversible covalent and irreversible covalent. Moleculesthat can participate in molecular binding include proteins, nucleicacids, carbohydrates, lipids, and small organic molecules such aspharmaceutical compounds. For example, proteins that form stablecomplexes with other molecules are often referred to as receptors whiletheir binding partners are called ligands. Nucleic acids can also formstable complex with themselves or others, for example, DNA-proteincomplex, DNA-DNA complex, DNA-RNA complex.

As used herein, the term “contacting” describes any suitable method ofbringing a first material in contact or physical association with asecond material. In some embodiments, the first material can be incontact with two or more materials. In some embodiments, contact betweenmaterials can be achieved through placing all materials in a suitablemedium, such as a solution.

The term “halogen” represents chlorine, fluorine, bromine, or iodine.The term “halo” represents chloro, fluoro, bromo, or iodo.

The terms “nucleic acid” and “nucleic acid molecule” are usedinterchangeably herein to refer to a polymeric form of nucleotides ofany length, and comprise ribonucleotides, deoxyribonucleotides, andanalogs or mixtures thereof. The terms include triple-, double- andsingle-stranded deoxyribonucleic acid (“DNA”), as well as triple-,double- and single-stranded ribonucleic acid (“RNA”). It also includesmodified, for example by alkylation, and/or by capping, and unmodifiedforms of the polynucleotide. More particularly, the terms“polynucleotide,” “oligonucleotide,” “nucleic acid,” and “nucleic acidmolecule” include polydeoxyribonucleotides (containing2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), includingtRNA, rRNA, hRNA, and mRNA, whether spliced or unspliced, any other typeof polynucleotide which is an N- or C-glycoside of a purine orpyrimidine base, and other polymers containing nonnucleotidic backbones,for example, polyamide (e.g., peptide nucleic acids (“PNAs”)) andpolymorpholino (commercially available from the Anti-Virals, Inc.,Corvallis, Oreg., as Neugene) polymers, and other syntheticsequence-specific nucleic acid polymers providing that the polymerscontain nucleobases in a configuration which allows for base pairing andbase stacking, such as is found in DNA and RNA. Thus, these termsinclude, for example, 3′-deoxy-2′,5′-DNA, oligodeoxyribonucleotide N3′to P5′ phosphoramidates, 2′-O-alkyl-substituted RNA, hybrids between DNAand RNA or between PNAs and DNA or RNA, and also include known types ofmodifications, for example, labels, alkylation, “caps,” substitution ofone or more of the nucleotides with an analog, inter-nucleotidemodifications such as, for example, those with uncharged linkages (e.g.,methyl phosphonates, phosphotriesters, phosphoramidates, carbamates,etc.), with negatively charged linkages (e.g., phosphorothioates,phosphorodithioates, etc.), and with positively charged linkages (e.g.,aminoalkylphosphoramidates, aminoalkylphosphotriesters), thosecontaining pendant moieties, such as, for example, proteins (includingenzymes (e.g. nucleases), toxins, antibodies, signal peptides,poly-L-lysine, etc.), those with intercalators (e.g., acridine,psoralen, etc.), those containing chelates (of, e.g., metals,radioactive metals, boron, oxidative metals, etc.), those containingalkylators, those with modified linkages (e.g., alpha anomeric nucleicacids, etc.), as well as unmodified forms of the polynucleotide oroligonucleotide. A nucleic acid generally will contain phosphodiesterbonds, although in some cases nucleic acid analogs may be included thathave alternative backbones such as phosphoramidite, phosphorodithioate,or methylphophoroamidite linkages; or peptide nucleic acid backbones andlinkages. Other analog nucleic acids include those with bicyclicstructures including locked nucleic acids, positive backbones, non-ionicbackbones and non-ribose backbones. Modifications of theribose-phosphate backbone may be done to increase the stability of themolecules; for example, PNA:DNA hybrids can exhibit higher stability insome environments. The terms “polynucleotide,” “oligonucleotide,”“nucleic acid” and “nucleic acid molecule” can comprise any suitablelength, such as at least 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 200,300, 400, 500, 1,000 or more nucleotides.

The term “metal” refers to alkali metals such as Li, Na or K, alkalineearth metals such as Ca or Mg, metalloids such as Al, as well aslanthanides, actinides, or transition metals.

As used herein, a “sample” can comprise a naturally occurring component,an artificially derived component, and/or a component artificiallysynthesized, in part or in whole. In some embodiments, the sample is abiological sample. In some embodiments, the sample comprises nucleicacid molecules, which can be from a biological sample or artificiallysynthesized and/or modified.

The term “biological sample” as used herein, refers to a sample obtainedfrom a biological subject, including samples of biological tissue orfluid origin obtained in vivo or in vitro. Such samples can be, but arenot limited to, body fluid (e.g., blood, blood plasma, serum, or urine),organs, tissues, stool, swab samples, and fractions and cells isolatedfrom mammals (e.g., humans). Biological samples also may includesections of the biological sample including tissues (e.g., sectionalportions of an organ or tissue). The term “biological sample” may alsoinclude extracts from a biological sample, for example, an antigen froma biological fluid (e.g., blood or urine). A biological sample may be ofprokaryotic origin (e.g., bacteria, archaea) or eukaryotic origin (e.g.,fungi, plants, insects, protozoa, birds, fish, reptiles). In someembodiments, the biological sample is mammalian (e.g., rat, mouse, cow,dog, donkey, guinea pig, or rabbit). In certain embodiments, thebiological sample is of primate origin (e.g., example, chimpanzee orhuman).

EXAMPLES Example 1: General Protocol for Acetate-Mediated Size Selectionof Nucleic Acids

The following protocol is for performing size-selection on a 50 μL PCRreaction. Larger volume reactions can be processed by scaling allreagents here proportionally.

Consumables & Reagents:

Borosilicate glass spin filters (MO BIO catalog #1200-50-SF)

SwiftMag® Beads

DNA Bind: 5.2 M guanidine hydrochloride, 30 mM Tris HCl, 8% isopropanol

Bind Modifier: 7.5 M ammonium acetate

Wash Buffer: 11.1 mM Tris buffer, pH 7.4-7.9, 1 mM EDTA, 108 mM NaCl,50% ethanol 100% ethanol

TABLE 1 Volumes of reagents for size selection reactions. Volumes (μL)of Reagent PCR reaction 50 50 50 50 50 Bind Modifier 15 20 25 30 35 DNABind 170 170 170 170 170 Base-pair cut-off obtained 100 200 400 16507000

Volumes of reagents needed for the size selection reactions are providedin Table 1. The volume of Bind Modifier (e.g., ammonium acetate) isadjusted to achieve different base pair cut-offs.

The above reagents are combined and mixed briefly by repeated pipetting(3-5×). Thereafter, the full volume is loaded onto a borosilicate glassspin filter and incubated for 2 minutes prior to centrifugation. Thespin filter is centrifuged for 30 seconds at 10,000×g. The flow throughcan be retained for further processing if the desired fragment size wasnegatively selected (i.e., not bound to the filter). For fragments boundto the spin filter, the filter is washed with 300 μL Wash Buffer via 2minutes of centrifugation at 16,000×g. Bound DNA fragments are theneluted with 50 μL of PCR-grade water or 10 mM Tris, pH 8.0 viacentrifugation at 16,000×g for 1 minute.

Example 2: Acetate-Mediated Size Selection of DNA on Borosilicate GlassSpin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 150 μL of DNA binding solution(5.2 M guanidine hydrochloride, 30 mM Tris-HCl, 8% isopropanol) and 25μL of DNA bind modifier (7.5 M ammonium acetate). A control sample wasmade by mixing the same amount of DNA ladder and DNA binding solutionwith 25 μL of PCR water. The reagents were mixed briefly by repeatedpipetting (3-5×). Thereafter, the full volume was loaded onto aborosilicate glass spin filter (MO BIO catalog #1200-50-SF) andincubated for 2 minutes prior to centrifugation. The spin filter wascentrifuged for 30 seconds at 10,000×g. The filter was then washed with300 μL of wash buffer (11.1 mM Tris, 1 mM EDTA, 108 mM NaCl, 50%ethanol; pH 7.4-7.9) via 2 minutes of centrifugation at 16,000×g. Thebound DNA fragments were eluted with 50 μL of PCR-grade water or 10 mMTris, pH 8.0 via centrifugation at 16,000×g for 1 minute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 1 compares the electrophoretic separation of a 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in theabsence of a DNA bind modifier (i.e., bands labeled “Bind only”) and inthe presence of the DNA bind modifier ammonium acetate (i.e., bandslabeled “Bind & −2”). This shows that the addition of ammonium acetate(“−2”) inhibits binding of DNA fragments below a certain molecularweight range (e.g., <400 bp).

Example 3: Effect of Increasing Acetate Concentration on Size Selectionof DNA on Borosilicate Glass Spin Fibers

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with varying volumes of DNA bindingsolution (5.2 M guanidine hydrochloride, 30 mM Tris-HCl, 8% isopropanol)and DNA bind modifier (7.5 M ammonium acetate). The reagents were mixedbriefly by repeated pipetting (3-5×). Thereafter, the full volume wasloaded onto a borosilicate glass spin filter (MO BIO catalog#1200-50-SF) and incubated for 2 minutes prior to centrifugation. Thespin filter was centrifuged for 30 seconds at 10,000×g. The filter wasthen washed with 300 μL of wash buffer (11.1 mM Tris, 1 mM EDTA, 108 mMNaCl, 50% ethanol; pH 7.4-7.9) via 2 minutes of centrifugation at16,000×g. The bound DNA fragments were eluted with 50 μL of PCR-gradewater or 10 mM Tris, pH 8.0 via centrifugation at 16,000×g for 1 minute.The eluents were analyzed by agarose gel electrophoresis.

FIG. 2 compares the electrophoretic separation of a 1 kb DNA molecularweight ladder subjected to an increasing amount of ammonium acetateduring the binding reaction using borosilicate glass spin filters. Thevarious ratios displayed on the gel (e.g., 5/110, 10/120) correspond tothe volume (μL) of 7.5 M ammonium acetate to the volume (μL) of DNAbinding solution (5.2 M Guanidine hydrochloride, 30 mM Tris-HCl, 8%isopropanol). The results of this experiment shows that increasing theamount of acetate during the binding reaction leads to an increasedmolecular weight cut-off of the nucleic acid molecules that bind to theborosilicate glass spin filters. A similar trend is observed when thevolume of the nucleic acid binding buffer is held constant and only theammonium acetate volume is changed (data not shown).

FIG. 3 compares the electrophoretic separation of a 1 kb DNA molecularweight ladder subjected to an increasing amount of ammonium acetateduring the binding reaction using borosilicate glass spin filters. Inthis gel, the nucleic acid binding solution was held constant at 170 Lwhile ammonium acetate volumes were varied from 0 to 35 μL. The resultsof this experiment show that increasing the amount of acetate during thebinding reaction leads to an increased molecular weight cut-off of thenucleic acid molecules that bind to the borosilicate glass spin filters.

Example 4: Acetate-Mediated Size Selection of DNA on Silica-CoatedMagnetic Beads

The same procedures performed above with borosilicate glass spin filterswere directly adapted to silica-coated (SwiftMag®) beads withoutmodification. Fifty microliters of a nucleic acid-containing sample(e.g., diluted 1 kb DNA molecular weight ladder) was mixed with varyingvolumes of DNA bind modifier (e.g., ammonium acetate) and DNA bindingsolution (e.g., 5.2 M Guanidine hydrochloride, 30 mM Tris-HCl, 8%isopropanol). To the mixture was added 25 μL of SwiftMag® beads, and thesample was mixed with gentle vortexing or orbital mixing for 2 minutes.The reaction was placed on an appropriate magnet to collect theSwiftMag® beads for 2 minutes. The collected beads were washed with 500μL of Wash Buffer and allowed to air dry for 5 minutes before beingsuspended in 50 μL of PCR-grade water (eluent) and incubated for 5minutes with vortexing or orbital mixing. The eluent was analyzed byagarose gel electrophoresis.

FIG. 4 compares electrophoretic separation of a 1 kb DNA molecularweight ladder samples contacted with silica-coated magnetic beads(SwiftMag® beads) in the presence or absence of ammonium acetate and inthe presence of absence of DNA binding solution (“Spin Bind”). In thepanel labeled “EtOH”, Spin Bind was substituted with an equal volume of100% ethanol, with or without ammonium acetate (“−2”). In the rightpanel (“Spin Bind”), DNA binding solution (5.2 M guanidinehydrochloride, 30 mM Tris HCl, 8% isopropanol) was used with or withoutammonium acetate. 50 μL of DNA ladder was combined with 200 μL DNABinding Solution (or ethanol) and L ammonium acetate. The results ofthis experiment indicate that the combination of Spin Bind and ammoniumacetate resulted in nucleic acid size selection.

FIG. 5 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples contacted with silica-coated magnetic beads in thepresence of different DNA bind modifiers. Ammonium acetate, lithiumacetate, water, potassium acetate, ammonium chloride, and sodium methanesulfonate were used as DNA bind modifiers. 50 μL of DNA ladder wascombined with 200 μL of DNA Binding Solution and 25 μL of the abovecompounds. Size selection was observed for all acetates, regardless ofthe cation (NH₄, Li⁺, K+). In contrast, removal of the acetate andretention of the ammonium cation, for example, did not result inobservable size selection.

Example 5: Double-Sided Acetate-Mediated Size Selection of Nucleic AcidsUsing Borosilicate Glass Fiber Matrix

An example of double-sided selection is given below. In this example,the double-sided selection of a 50 μL PCR reaction is carried out toisolate DNA fragments between 400 and 1650 base pairs.

Bind Fragments>1650 bp:

To a solution of 150 μL of DNA Bind and 25 μL of Bind Modifier (e.g.,ammonium acetate) is added 50 μL of a PCR sample. The full volume of thesolution mixture is loaded onto a borosilicate glass spin filter andincubated 2 minutes prior to centrifugation. The spin filter iscentrifuged for 30 seconds at 10,000×g, and the filtrate (containingfragments <1650 bp) is collected for further processing. The spin filter(containing fragments >1650 bp) is discarded.

Bind Fragments≥400 bp<1650 bp:

An equal volume of 100% ethanol is added to the filtrate from the stepabove, and this solution is applied to a fresh spin filter. The sampleis centrifuged for 30 seconds at 10,000×g, and the filtrate isdiscarded. The filter is washed with 300 μL Wash Buffer, spun dry andthe DNA is eluted with 50 μL of PCR-grade water. Then, 140 μL of DNABind and 20 μL of Bind Modifier (i.e., ammonium acetate) are added tothe eluted DNA. The entire volume of the mixture is loaded on the samespin filter used in the previous step and centrifuged for 30 seconds at10,000×g. The filtrate is discarded, and the spin filter is washed with300 μL Wash Buffer, spun dry and the DNA is eluted with 50 μL ofPCR-grade water.

Example 6: Double-Sided Acetate-Mediated Size Selection of Nucleic AcidsUsing Silica-Coated Magnetic Beads

The same procedures performed above with borosilicate glass spin filtersare directly adapted to silica-coated (SwiftMag®) beads withoutmodification. In this example, the double-sided selection of a 50 μL PCRreaction is carried out to isolate DNA fragments between 400 and 1650base pairs:

Bind Fragments>1650 bp:

To a solution of 150 μL of DNA Bind and 25 μL of Bind Modifier (e.g.,ammonium acetate) is added 50 μL a PCR sample. To the mixture is added25 μL of SwiftMag® beads, and the sample is mixed with gentle vortexingor orbital mixing for 2 minutes. The reaction is placed on anappropriate magnet to collect the SwiftMag® beads for 2 minutes. Thesupernatant is removed and retained, and the collected beads (containingfragments >1650 bp) are discarded.

Bind Fragments≥400 bp<1650 bp:

An equal volume of 100% ethanol is added to the supernatant and a freshaliquot of SwiftMag® beads (25 μL). The sample is mixed as above andcollected on a magnet for 2 minutes. The supernatant is removed, and thesamples are removed from the magnet. The bound DNA is eluted with 50 μLof PCR-grade water. With the SwiftMag® beads still present, 140 μL ofDNA Bind and 20 μL of Bind Modifier are added to the eluted DNA, andreaction is mixed for 2 minutes. The reaction is placed on anappropriate magnet to collect the SwiftMag® beads for 2 minutes. Thesupernatant is removed, and the beads are washed with 500 μL of WashBuffer. The beads are collected on a magnet, and the supernatant isremoved. The beads are allowed to air dry for 5 minutes before beingsuspended in 50 μL of PCR-grade water and incubated for 5 minutes withvortexing or orbital mixing. The samples are placed back on a magnet for2 minutes, and the eluent is transferred to the new tubes.

Example 7: Effect of Different Alkali Metal Cation Acetates on SizeSelection of DNA on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding solutionand 0-35 μL of each DNA bind modifier. A control sample was made bymixing the same amount of DNA ladder and DNA binding solution withoutDNA bind modifier. Ammonium acetate, sodium acetate, lithium acetate,cesium acetate, rubidium acetate, and potassium acetate were used as DNAbind modifiers. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The filter was then washed with 300 μL of wash buffer via 1minute of centrifugation at 10,000×g. The spin filter was centrifugedagain for 2 minutes at 16,000×g to spin dry. The bound DNA fragmentswere incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 6A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium acetate, and lithium acetate (0-35 μL)were used as DNA bind modifiers in this gel.

FIG. 6B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, cesium acetate, ribidium acetate, andpotassium acetate (0-35 μL) were used as DNA bind modifiers in this gel.

Example 8: Effect of Different Ammonium Acetates on Size Selection ofDNA on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding solutionand 0-35 μL of each DNA bind modifier. A control sample was made bymixing the 50 μL DNA ladder and 170 μL of DNA binding solution withoutDNA bind modifier. 7.5 M ammonium acetate, 6.3 M tetramethyl ammoniumacetate, 3.44 M tetramethyl ammonium acetate tetrahydrate, 3.12 Mtetramethyl ammonium acetate, 4.67 M tetramethyl ammonium acetate, and6.23 M tetramethyl ammonium acetate were used as DNA bind modifiers. Thefull volume of the reagents was loaded onto a borosilicate glass spinfilter and incubated for 2 minutes prior to centrifugation. The spinfilter was centrifuged for 1 minute at 10,000×g. The filter was thenwashed with 500 μL of wash buffer via 1 minute of centrifugation at10,000×g. The spin filter was centrifuged again for 2 minutes at16,000×g to spin dry. The bound DNA fragments were incubated with 50 μLof elution buffer for 2 minutes and centrifuged at 10,000×g for 1 minuteto elute. The eluents were analyzed by agarose gel electrophoresis.

FIG. 7A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. 7.5 M ammonium acetate, 6.3 M tetramethyl ammonium acetate, and3.44 M tetramethyl ammonium acetate tetrahydrate were used as DNA bindmodifiers in this gel.

FIG. 7B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. 7.5 M ammonium acetate, 3.12 M tetramethyl ammonium acetate,4.67 M tetramethyl ammonium acetate, and 6.23 M tetramethyl ammoniumacetate were used as DNA bind modifiers in this gel. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were 0, 25 and 35 μL.

Example 9: Effect of Different Ammonium Anions on Size Selection of DNAon Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding solutionand 35 μL of each DNA bind modifier. A control sample was made by mixingthe 50 μL DNA ladder and 170 μL of DNA binding solution without DNA bindmodifier. Tetramethyl ammonium acetate (4.7 M), ammonium phosphatedibasic (4.03 M), choline chloride (5.68 M),Tris(2-hydroxyethyl)methylammonium methylsulfate (TMAMS), ammoniumsulfate, 2.02 M diammonium phosphate (DAP), and 2.42 M DAP were used asDNA bind modifiers. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The filter was then washed with 500 μL of wash buffer via 1minute of centrifugation at 10,000×g. The spin filter was centrifugedagain for 2 minutes at 16,000×g to spin dry. The bound DNA fragmentswere incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 8A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of different DNA bindmodifiers during the binding reaction using borosilicate glass spinfilters. Sample A contained 1 kb DNA molecular weight ladder sample inthe absence of any DNA bind modifiers. Tetramethyl ammonium acetate (4.7M), ammonium phosphate dibasic (4.03 M), choline chloride (5.68 M),Tris(2-hydroxyethyl)methylammonium methylsulfate (TMAMS), and ammoniumsulfate were used as DNA bind modifiers (4.4 M) in this gel.

FIG. 8B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of increasing amounts of DAPduring the binding reaction using borosilicate glass spin filters. Inthis gel, 2.02 M DAP and 2.42 M DAP were used as DNA bind modifiers.

FIG. 8C compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of diammonium phosphate(DAP) during the binding reaction using borosilicate glass spin filterssubject to selection and different stages. 2.42 M DAP was used as DNAbind modifier in samples B, C, and D. Sample A contained the 1 kb DNAmolecular weight ladder sample in the absence of any DNA bind modifiers.Samples B was 1 kb DNA molecular weight ladder passed through aborosilicate glass spin filter in the presence of 35 μL of 2.42 M DAP.Sample C was the recovered flow through of 1 kb DNA molecular weightladder passed through a borosilicate glass spin filter in the presenceof 35 μL of 2.42 M DAP mixed with ethanol. Sample D contained the 1 kbDNA molecular weight ladder sample in the absence of any DNA bindmodifiers bound to the filter that was then subjected to selection with35 μL of 2.42 M DAP (‘on-filter selection’).

Example 10: Double-Sided Acetate-Mediated Size Selection of NucleicAcids Using Borosilicate Glass Filters

In cases where target DNA fragments were mixed with both larger andsmaller DNA fragments, the target DNA fragments in the middle range wereisolated with a double sided approach involving a two-step process. Forcontrol, Sample A contained 50 μL of a nucleic acid-containing sample(diluted 1 kb DNA molecular weight ladder) mixed with 170 μL of DNAbinding solution and no Bind Modifier. The sample was centrifuged for 1minute at 10,000×g, and the filtrate discarded. The filter was washedwith 500 μL wash buffer and centrifuged at 10,000×g for 1 minute. Thecolumn was then spun dry via centrifugation at 16,000×g for 2 minutes.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

Bind Fragments Larger than the Target Range in Primary Spin Column:

Samples B and C were 1 kb DNA molecular weight ladder passed through aborosilicate glass spin filter in the presence of 35 μL and 25 μL,respectively, of 4.7 M tetramethyl ammonium acetate. The sample wascentrifuged for 1 minute at 10,000×g, and the filtrate discarded. Thefilter was washed with 500 μL wash buffer and centrifuged at 10,000×gfor 1 minute. The column was then spun dry via centrifugation at16,000×g for 2 minutes. The bound DNA fragments were incubated with 50μL of elution buffer for 2 minutes and centrifuged at 10,000×g for 1minute to elute. The eluents were analyzed by agarose gelelectrophoresis. Sample D was the recovered flow through of 1 kb DNAmolecular weight ladder that passed through a borosilicate glass spinfilter in the presence of 35 μL of 4.7 M tetramethyl ammonium acetatewith a single volume of ethanol added. This sample was added to a newspin column and centrifuged for 1 minute at 10,000×g. The filter waswashed with 500 μL wash buffer and centrifuged at 10,000×g for 1 minute.The column was then spun dry via centrifugation at 16,000×g for 2minutes. The bound DNA fragments were incubated with 50 μL of elutionbuffer for 2 minutes and centrifuged at 10,000×g for 1 minute to elute.The eluents were analyzed by agarose gel electrophoresis.

Sample E was subjected to two selection steps. In the first selectionstep, 400 μL of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 680 aL of DNA binding solutionand 140 μL Bind Modifier (e.g., 4.7 M tetramethyl ammonium acetate). 305μL of the solution mixture was loaded onto a borosilicate glass spinfilter and incubated 2 minutes prior to centrifugation. The spin filterwas centrifuged for 1 minute at 10,000×g, and the filtrate (containingfragments smaller than the target) was collected for further processing.The spin filter (containing fragments larger than the target) wasdiscarded.

Remove Fragments Smaller than the Target Range in Secondary Spin Column:

For the second selection step of Sample E, an equal volume of 100%ethanol was added to the filtrate collected from the step above, andthis solution was applied to a fresh spin filter. The sample wascentrifuged for 1 minute at 10,000×g, and the filtrate discarded. Amixture of 25 μL 4.7 M tetramethyl ammonium acetate and 170 μL of DNAbinding solution was added to the filter. The sample was thencentrifuged for 1 minute at 10,000×g and the filtrate discarded. Thefilter was washed with 500 μL wash buffer and centrifuged at 10,000×gfor 1 minute. The column was then spun dry via centrifugation at16,000×g for 2 minutes. The bound DNA fragments were incubated with 50μL of elution buffer for 2 minutes and centrifuged at 10,000×g for 1minute to elute. The eluents were analyzed by agarose gelelectrophoresis.

FIG. 9A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the binding reaction using borosilicate glass spin filterssubject to one or more steps of selection. Sample A contained the 1 kbDNA molecular weight ladder sample in the absence of any DNA bindmodifiers. In samples B, C, D, and E, 4.7 M tetramethyl ammonium acetatewas used as DNA bind modifier. Samples B and C were 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in thepresence of 35 μL and 25 μL, respectively, of 4.7 M tetramethyl ammoniumacetate. Sample D was the recovered flow through of 1 kb DNA molecularweight ladder passed through a borosilicate glass spin filter in thepresence of 35 μL of 4.7 M tetramethyl ammonium acetate (Sample B); theflow through was bound to a spin filter with ethanol, washed and eluted.Sample E was the flow through of 1 kb DNA molecular weight ladder passedthrough a borosilicate glass spin filter in the presence of 35 μL of 4.7M tetramethyl ammonium acetate; the collected flow through was bound toa spin filter with ethanol, as in Sample D, and subjected to a secondstep of selection with 25 μL of 4.7 M tetramethyl ammonium acetate.

Example 11: Double-Sided Acetate-Mediated Size Selection of NucleicAcids Using Silica-Coated Magnetic Beads

In cases where target DNA fragments were mixed with both larger andsmaller DNA fragments, the target DNA fragments in the middle range wasisolated with a double sided approach involving a two-step process usingsilica-coated (SwiftMag®) beads. For control, Sample A contained 50 μLof a nucleic acid-containing sample (diluted 1 kb DNA molecular weightladder) mixed with 170 μL of DNA binding solution, no Bind Modifier, and25 μL of SwiftMag® beads. The sample was mixed by vortexing every 2minutes for 10 minutes, then placed on an appropriate magnet to collectthe SwiftMag® beads for 2 minutes. The supernatant was removed, and thebeads were washed with 500 μL of Wash Buffer. The beads were collectedon a magnet, and the supernatant was removed. The beads were incubatedwith lids open for 20 minutes on the magnetic rack before beingsuspended in 50 μL of elution buffer water and mixed by vortexing every2 minutes for 10 minutes. The samples were placed back on a magnet andthe eluent was transferred to the new tubes. The eluents were analyzedby agarose gel electrophoresis.

Bind Fragments Larger than the Target Range in Primary Spin Column:

Samples B and C were 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence 20 μL and 25 μL,respectively, of 4.7 M tetramethyl ammonium acetate. The supernatant wasremoved, and the beads were washed with 500 μL of Wash Buffer. The beadswere collected on a magnet, and the supernatant was removed. The beadswere incubated with lids open for 20 minutes on the magnetic rack beforebeing suspended in 50 μL of elution buffer water and mixed by vortexingevery 2 minutes for 10 minutes. The samples were placed back on a magnetand the eluent was transferred to the new tubes. The eluents wereanalyzed by agarose gel electrophoresis. Sample D was the recoveredsupernatant of 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence of 25 μL of 4.7 Mtetramethyl ammonium acetate. The supernatant was transferred to a cleantube, 245 μL ethanol and L of SwiftMag® beads was added to this tube.The sample was mixed by vortexing every 2 minutes for 10 minutes, thenplaced on an appropriate magnet to collect the SwiftMag® beads for 2minutes. The supernatant was then removed, and the beads were washedwith 500 μL of Wash Buffer. The beads were collected on a magnet, andthe supernatant was removed. The beads were incubated with lids open for20 minutes on the magnetic rack before being suspended in 50 μL ofelution buffer water and mixed by vortexing every 2 minutes for 10minutes. This sample was placed back on a magnet and the eluent wastransferred to the new tubes. The eluents were analyzed by agarose gelelectrophoresis.

Sample E was subjected to two selection steps. In the first selectionstep, 50 μL of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 L of DNA binding solutionand 25 μL Bind Modifier (4.7 M tetramethyl ammonium acetate). To themixture, 25 μL of SwiftMag® beads was added, and the sample was mixed byvortexing every 2 minutes for 10 minutes. The reaction was placed on anappropriate magnet to collect the SwiftMag® beads for 2 minutes. Thesupernatant was removed and retained, and the collected beads(containing fragments larger than the target) were discarded.

Remove Fragments Smaller than the Target Range in Secondary Spin Column:

In the second selection step of Sample E, 245 μL of 100% ethanol and afresh aliquot of SwiftMag® beads (25 μL) was added to the supernatant.The sample was mixed by vortexing every 2 minutes for 10 minutes andcollected on a magnet for 2 minutes. The supernatant was removed, andthe samples were removed from the magnet. With the SwiftMag® beads stillpresent, 50 μL of water, 170 μL of DNA binding solution, and 20 μL of4.7 M tetramethyl ammonium acetate were added to the pellet, andreaction was mixed by vortexing every 2 minutes for 10 minutes. Thereaction was placed on an appropriate magnet to collect the SwiftMag®beads for 2 minutes. The supernatant was removed, and the beads werewashed with 500 μL of Wash Buffer. The beads were collected on a magnet,and the supernatant was removed. The beads were incubated with lids openfor 20 minutes on the magnetic rack before being suspended in 50 μL ofelution buffer water and mixed by vortexing every 2 minutes for 10minutes. The samples were placed back on a magnet and the eluent wastransferred to the new tubes. The eluents were analyzed by agarose gelelectrophoresis.

FIG. 9B compares electrophoretic separation of 1 kb DNA molecular weightladder samples contacted with silica-coated magnetic beads (SwiftMag®beads) in the presence or absence of 4.7 M tetramethyl ammonium acetatesubject to one or more steps of selection. Tetramethyl ammonium acetateat 4.7 M was used as DNA bind modifier in samples B, C, D, and E.Samples B and C were 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence 20 μL and 25 μL,respectively, of 4.7 M tetramethyl ammonium acetate. Sample D was therecovered supernatant of 1 kb DNA molecular weight ladder contacted withsilica-coated magnetic beads in the presence of 25 μL of 4.7 Mtetramethyl ammonium acetate. Sample E was the recovered supernatant of1 kb DNA molecular weight ladder contacted with silica-coated magneticbeads in the presence of 25 μL of 4.7 M tetramethyl ammonium acetatethat was then washed and subjected to a second step of selection with 20μL of 4.7 M tetramethyl ammonium acetate.

Example 12: Effect of Different Concentrations of Ammonium Anions onSize Selection of DNA on Borosilicate Glass Spin Filters with andwithout Normalization

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of ammonium acetate asDNA binding solution and 0-35 μL of each DNA bind modifier. A controlsample was made by mixing the same amount of DNA ladder and DNA bindingsolution without DNA bind modifier. Each of the normalized samples had45-80 μL of water added to achieve a water and ammonium acetate totalvolume of 80 μL. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The filter was then washed with 300 μL of wash buffer via 1minute of centrifugation at 10,000×g. The spin filter was centrifugedagain for 2 minutes at 16,000×g to spin dry. The bound DNA fragmentswere incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 10A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier (ammonium acetate) during the binding reaction usingborosilicate glass spin filters. The amount of ammonium acetate was notnormalized against a standard volume of the nucleic binding buffer. Inthis gel, the nucleic acid binding solution was held constant at 170 μLwhile DNA bind modifier volumes were varied from 0 to 35 μL.

FIG. 10B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier (ammonium acetate) during the binding reaction usingborosilicate glass spin filters. The amount of nucleic acid bindingbuffer and ammonium acetate was normalized against a standard volumeusing water. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while DNA bind modifier volumes were varied from 0 to35 μL.

Example 13: Effect of Substituted Carboxylates on Size Selection of DNAon Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding solutionand 0-35 μL of each DNA bind modifier. A control sample was made bymixing the same amount of DNA ladder and DNA binding solution withoutDNA bind modifier. Ammonium acetate, sodium formate, sodium propionate,sodium trifluoroacetate, and sodium trichloroacetate were used as DNAbind modifiers. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The filter was then washed with 300 μL of wash buffer via 1minute of centrifugation at 10,000×g. The spin filter was centrifugedagain for 2 minutes at 16,000×g to spin dry. The bound DNA fragmentswere incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 11A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium formate, and sodium propionate wereused as DNA bind modifiers. In this gel, the nucleic acid bindingsolution was held constant at 170 μL while DNA bind modifier volumeswere varied from 0 to 35 μL.

FIG. 11B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of different DNAbind modifiers during the binding reaction using borosilicate glass spinfilters. Ammonium acetate, sodium trifluoroacetate, and sodiumtrichloroacetate were used as DNA bind modifiers. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 35 μL.

Example 14: Effect of Different DNA Binding Solutions on Size Selectionof DNA on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of different DNA bindingsolution and either 0 or 35 μL of DNA bind modifier. 4.67 M tetramethylammonium acetate was used as DNA bind modifier. Bind A (Guanidine HCl(5.2 M) [50%]+Tris HCl (0.03 M)+99% Isopropanol (8%)), Bind B (GuanidineThiocyanate (4 M) [47%]+Tris Base (0.1M)+33% Ethanol), Bind C (GuanidineThiocyanate (6 M, 71%)), and Bind D (2.3 Guan+0.0128 Tris HCl+3.88%isoprop)+56% EtOH) were used as DNA binding solutions. The full volumeof the reagents was loaded onto a borosilicate glass spin filter andincubated for 2 minutes prior to centrifugation. The spin filter wascentrifuged for 1 minute at 10,000×g. The filter was then washed with500 μL of wash buffer via 1 minute of centrifugation at 10,000×g. Thespin filter was centrifuged again for 2 minutes at 16,000×g to spin dry.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 12 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different DNA binding solutions inthe presence or absence of DNA bind modifier (4.67 M tetramethylammonium acetate) during the binding reaction using borosilicate glassspin filters. In this gel, the nucleic acid binding solution was heldconstant at 170 μL, DNA bind modifier volumes was either 0 or 35 μL.

Example 15: Effect of Different Guanidine Based DNA Binding Solutions onSize Selection of DNA on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of different DNA bindingsolutions and either 0 or 35 μL of DNA bind modifier. 4.67 M tetramethylammonium acetate was used as DNA bind modifier. Guanidine carbonate,guanidine phosphate, guanidine sulfate, and guanidine thiocyanate basedsolutions were used as DNA binding solutions. The full volume of thereagents was loaded onto a borosilicate glass spin filter and incubatedfor 2 minutes prior to centrifugation. The spin filter was centrifugedfor 1 minute at 10,000×g. The filter was then washed with 500 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 13 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different DNA binding solutions inthe presence or absence of DNA bind modifier (4.67 M tetramethylammonium acetate) during the binding reaction using borosilicate glassspin filters. Guanidine carbonate, guanidine phosphate, guanidinesulfate, and guanidine thiocyanate based solutions were used as DNAbinding solutions. In this gel, the nucleic acid binding solution washeld constant at 170 μL, DNA bind modifier volumes was either 0 or 35μL.

Example 16: Effect of Ammonium Acetate on Size Selection of gDNA onBorosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder or diluted E. coli gDNA) was mixed with 170 μLof different DNA binding solution and 0 to 35 μL of DNA bind modifier.4.67 M tetramethyl ammonium acetate was used as DNA bind modifier. Thefull volume of the reagents was loaded onto a borosilicate glass spinfilter and incubated for 2 minutes prior to centrifugation. The spinfilter was centrifuged for 1 minute at 10,000×g. The filter was thenwashed with 500 μL of wash buffer via 1 minute of centrifugation at10,000×g. The spin filter was centrifuged again for 2 minutes at16,000×g to spin dry. The bound DNA fragments were incubated with 50 μLof elution buffer for 2 minutes and centrifuged at 10,000×g for 1 minuteto elute. The eluents were analyzed by agarose gel electrophoresis.

FIG. 14 compares the electrophoretic separation of 1 kb DNA molecularweight ladder and E. coli gDNA samples subjected to increasing amountsof 4.67 M tetramethyl ammonium acetate as DNA bind modifier during thebinding reaction using borosilicate glass spin filters. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 35 μL.

Example 17: Effect of Ammonium Acetate on Size Selection of PrimerDimers on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder or diluted PCR reaction) was mixed with 170 μLof DNA binding solution and 0-25 aL of DNA bind modifier. 4.7 Mtetramethyl ammonium acetate was used as DNA bind modifier. The fullvolume of the reagents was loaded onto a borosilicate glass spin filterand incubated for 2 minutes prior to centrifugation. The spin filter wascentrifuged for 1 minute at 10,000×g. The filter was then washed with500 μL of wash buffer via 1 minute of centrifugation at 10,000×g. Thespin filter was centrifuged again for 2 minutes at 16,000×g to spin dry.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 15A shows the electrophoretic separation of PCR reactions generatedusing appropriate primers.

FIG. 15B compares the electrophoretic separation of 1 kb DNA molecularweight ladder and PCR product samples subjected to increasing amounts of4.7 M tetramethyl ammonium acetate as DNA bind modifier during thebinding reaction using borosilicate glass spin filters. In this gel, thenucleic acid binding solution was held constant at 170 μL while DNA bindmodifier volumes were varied from 0 to 25 μL.

Example 18: Effect of Ethanol as Secondary Bind for Recovered FlowThrough of Ammonium Acetate Size Selected DNA on Borosilicate Glass SpinFilters

Samples of 50 μL of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder was mixed with 170 μL of DNA binding solutionand 35 μL of DNA bind modifier. 4.7 M tetramethyl ammonium acetate wasused as DNA bind modifier. A control with no selection was prepared with50 μL of a nucleic acid-containing sample mixed with 170 μL of DNAbinding solution. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The control with no selection and spin filter from initialbind was set aside. The flow through of samples with DNA bind modifierwas recovered and combined with 1 volume, 2 volumes, or 3 volumes ofneat EtOH by vortexting. The EtOH and recovered flow through mixtureswere loaded onto separate secondary spin columns and centrifuged for 1minute at 10,000×g. The filters were then washed with 500 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 16 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the initial binding reaction using borosilicate glass spinfilters further subjected to a secondary bind. Different volumes ofethanol were used as secondary bind. Samples in lanes 1 and 2 containedthe 1 kb DNA molecular weight ladder sample in the absence of any DNAbind modifiers. Samples in lanes 3-10 contained 35 μL of 4.7 Mtetramethyl ammonium acetate used as DNA bind modifier in the initialbind. Samples in lanes 5-10 were the recovered flow through of 1 kb DNAmolecular weight ladder passed through a borosilicate glass spin filterin the presence of 35 μL of 4.7 M tetramethyl ammonium acetate subjectedto a secondary bind using different volumes of neat ethanol.

Example 19: Effect of Simultaneous Vs. Stepwise Selection of DNA onBorosilicate Glass Spin Filters

The simultaneous selection strategy was performed by first combiningnucleic acid-containing sample, DNA binding buffer, and DNA bindmodifier in solution and then passing this solution through a spinfilter to bind a range of molecular weights. 50 μL of a nucleicacid-containing sample (diluted 1 kb DNA molecular weight ladder) wasmixed with 170 μL of DNA binding solution and 0-35 μL of 4.7 tetramethylammonium acetate as DNA bind modifier. The full volume of the reagentswas loaded onto a borosilicate glass spin filter and incubated for 2minutes prior to centrifugation. The spin filter was centrifuged for 1minute at 10,000×g. The filter was then washed with 500 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

The stepwise binding strategy was performed by first binding the nucleicacid-containing sample to a spin filter (using DNA binding solutionwithout DNA bind modifier) and second, washing the spin filter with amixture of DNA binding solution and DNA bind modifier (on-filterselection). First, 50 μL of a nucleic acid-containing sample (diluted 1kb DNA molecular weight ladder) mixed with 170 μL of DNA binding bufferwas loaded onto a borosilicate glass spin filter. The spin filter wascentrifuged for 1 minute at 10,000×g and the flow through was discarded.Second, a mixture of 170 μL of DNA binding buffer and 0-35 μL of 4.7tetramethyl ammonium acetate as DNA bind modifier was loaded onto thespin filter. The filter and mixture was incubated for 2 minutes prior tocentrifugation then centrifuged for 1 minute at 10,000×g. The filter waswashed with 500 μL of wash buffer via 1 minute of centrifugation at10,000×g. The spin filter was centrifuged again for 2 minutes at16,000×g to spin dry. The bound DNA fragments were incubated with 50 μLof elution buffer for 2 minutes and centrifuged at 10,000×g for 1 minuteto elute. The eluents were analyzed by agarose gel electrophoresis.

FIG. 17 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of increasing amounts of 4.67 Mtetramethyl ammonium acetate as DNA bind modifiers using borosilicateglass spin filters with a simultaneous selection strategy and a stepwiseselection strategy. DNA bind modifier was added to the DNA sample priorto loading on the spin filter for simultaneous selection and added tothe spin filter bound with DNA for stepwise selection (on-filterselection). In this gel, DNA bind modifier volumes were varied from 0 to35 μL.

Example 20: Effect of Stepwise Selection of DNA on Borosilicate GlassSpin Filters for Eliminating Low Molecular Weight DNA

For the initial binding reaction, 50 μL of a nucleic acid-containingsample (diluted 1 kb DNA molecular weight ladder) was mixed with 170 μLof DNA binding buffer and 0, 25 or 35 μL of 4.7 tetramethyl ammoniumacetate as DNA bind modifier. The filter and mixture was incubated for 2minutes prior to centrifugation then centrifuged for 1 minute at10,000×g. The flow through was combined with an equal volume of neatethanol and set aside (Sample C). For the secondary binding reaction,170 μL of DNA binding buffer and 25 or 35 μL of 4.7 tetramethyl ammoniumacetate as DNA bind modifier was loaded into the column (Sample B). Thefilter and mixture was incubated for 2 minutes prior to centrifugationthen centrifuged for 1 minute at 10,000×g. The flow through was combinedwith an equal volume of neat ethanol and set aside (Sample D). Samples Cand D were added to a new spin column and incubated for 2 minutes, thencentrifuged for 1 minute at 10,000×g. All samples were washed with 500μL of wash buffer via 1 minute of centrifugation at 10,000×g. The spinfilter was centrifuged again for 2 minutes at 16,000×g to spin dry. Thebound DNA fragments were incubated with 50 μL of elution buffer for 2minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 18 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence of different amounts of 4.67 Mtetramethyl ammonium acetate as DNA bind modifier using borosilicateglass spin filters in a stepwise binding method. Sample A was 1 kb DNAmolecular weight ladder subjected to 4.7 M tetramethyl ammonium acetateduring an initial binding reaction using borosilicate glass spinfilters. Sample B was 1 kb DNA molecular weight ladder subjected to 4.7M tetramethyl ammonium acetate during an initial binding reaction usingborosilicate glass spin filters subjected to a secondary bindingreaction using the same DNA bind modifier. Sample C was the recoveredflow through of Sample A. Sample D was the recovered flow through ofSample B. In this gel, the nucleic acid binding solution was heldconstant at 170 μL while DNA bind modifier volumes were varied from 25to 35 μL.

Example 21: Effect of Different Concentrations of Ethanol as SecondaryBind for Recovered Flow Through of Ammonium Acetate Size Selected DNA onBorosilicate Glass Spin Filters

Samples of 50 μL of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder was mixed with 170 μL of DNA binding buffer and35 μL of DNA bind modifier. 4.7 M tetramethyl ammonium acetate was usedas DNA bind modifier. A control with no selection was prepared with 50μL of a nucleic acid-containing sample mixed with 170 μL of DNA bindingbuffer. The full volume of the reagents was loaded onto a borosilicateglass spin filter and incubated for 2 minutes prior to centrifugation.The spin filter was centrifuged for 1 minute at 10,000×g. The controlwith no selection and spin filter from initial bind was set aside. Theflow through of samples with DNA bind modifier was recovered andcombined with 50%, 70%, 90%, or 100% EtOH. The EtOH and recovered flowthrough mixtures were loaded onto separate secondary spin columns andcentrifuged for 1 minute at 10,000×g. The filters were then washed with500 μL of wash buffer via 1 minute of centrifugation at 10,000×g. Thespin filter was centrifuged again for 2 minutes at 16,000×g to spin dry.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 19 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifiersduring the initial binding reaction using borosilicate glass spinfilters and further subjected to a secondary bind. Differentconcentrations of ethanol were used as secondary bind. Samples in lanes1 and 2 contained the 1 kb DNA molecular weight ladder sample in theabsence of any DNA bind modifiers. Samples in lanes 3-12 contained 35 μL4.7 M tetramethyl ammonium acetate used as DNA bind modifier in theinitial bind. Samples in lanes 5-12 were the recovered flow through of 1kb DNA molecular weight ladder passed through a borosilicate glass spinfilter in the presence of 35 μL of 4.7 M tetramethyl ammonium acetatesubjected to a second bind using different concentrations of ethanol.

Example 22: Effect of Diluting Recovered Flow Through of AmmoniumAcetate Size Selected DNA on Borosilicate Glass Spin Filters DuringSecondary Bind

Samples of 50 μL of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder was mixed with 170 μL of DNA binding buffer and35 μL of DNA bind modifier. 4.7 M tetramethyl ammonium acetate was usedas DNA bind modifier. A control with no selection was prepared with 50μL of a nucleic acid-containing sample mixed with 170 μL of DNA bindingbuffer. The full volume of the reagents was loaded onto a borosilicateglass spin filter and incubated for 2 minutes prior to centrifugation.The spin filter was centrifuged for 1 minute at 10,000×g. The controlwith no selection and spin filter from initial bind was set aside. Theflow through of samples with DNA bind modifier was recovered andcombined with nothing, 1 volume of neat ethanol, 1 volume of water, 2volumes of water, or 3 volumes of water. The recovered flow throughmixtures were loaded onto separate secondary spin columns andcentrifuged for 1 minute at 10,000×g. The filters were then washed with500 μL of wash buffer via 1 minute of centrifugation at 10,000×g. Thespin filter was centrifuged again for 2 minutes at 16,000×g to spin dry.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 20A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifier(4.67 M tetramethyl ammonium acetate) during the initial bindingreaction using borosilicate glass spin filters and further subjected toa secondary bind. During the secondary bind, the flow through was notmixed with other solutions, mixed with ethanol, or with mixed withwater.

FIG. 20B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifier(4.67 M tetramethyl ammonium acetate) during the initial bindingreaction using borosilicate glass spin filters and further subjected toa secondary bind. During the secondary bind, the flow through wasdiluted with 1 volume of water, 2 volumes of water, 3 volumes of wateror 1 volume of EtOH.

Example 23: Effect of DNA Binding Buffers with Different Guanidine HClConcentrations on DNA Binding on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of different DNA bindingbuffers. DNA binding buffers with 0.375 M, 0.75 M, 1.5 M, 2 M, and 3 Mguanidine HCl concentrations were used. The full volume of the reagentswas loaded onto a borosilicate glass spin filter and incubated for 2minutes prior to centrifugation. The spin filter was centrifuged for 1minute at 10,000×g. The filter was then washed with 500 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 21A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding buffers with differentguanidine HCl concentrations during the binding reaction usingborosilicate glass spin filters. Nucleic acid binding buffers with 1.5M, 2 M, and 3 M Guanidine HCl were used. In this gel, the differentnucleic acid binding solutions was held constant at 170 μL and DNAsample was held constant at 50 μL.

FIG. 21B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding buffers with differentguanidine HCl concentrations during the binding reaction usingborosilicate glass spin filters. Nucleic acid binding buffers with 0.375M, 0.75 M, and 1.5 M guanidine HCl were used. In this gel, the differentnucleic acid binding solutions was held constant at 170 μL and DNAsample was held constant at 50 μL.

Example 24: Effect of Different Tetramethyl Ammonium AcetateConcentrations on Size Selection of DNA on Borosilicate Glass SpinFilters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding buffer and0-35 μL of each concentration of DNA bind modifier. A control sample wasmade by mixing the 50 μL DNA ladder and 170 μL of DNA binding bufferwithout DNA bind modifier. 4.7 M, 3.8 M, and 3 M tetramethyl ammoniumacetate were used as DNA bind modifiers. The full volume of the reagentswas loaded onto a borosilicate glass spin filter and incubated for 2minutes prior to centrifugation. The spin filter was centrifuged for 1minute at 10,000×g. The filter was then washed with 300 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 22A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to different concentrations of DNA bindmodifier during the binding reaction using borosilicate glass spinfilters. Increasing amounts of 4.7 M and 3.8 M tetramethyl ammoniumacetate were used as DNA bind modifiers. In this gel, the nucleic acidbinding solution was held constant at 170 μL while DNA bind modifiervolumes were varied from 0 to 35 μL.

FIG. 22B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to increasing amounts of DNA bindmodifier during the binding reaction using borosilicate glass spinfilters. 3 M tetramethyl ammonium acetate was used as DNA bind modifier.In this gel, the nucleic acid binding solution was held constant at 170μL while DNA bind modifier volumes were varied from 0 to 35 μL.

Example 25: Effect of DNA Binding Buffers with Different Guanidine HClConcentrations on Size Selection of DNA on Borosilicate Glass SpinFilters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of different DNA bindingsolutions and 0-35 μL of 4.7 M tetramethyl ammonium acetate. StandardDNA binding solution and DNA binding solutions with 1.5 M and 3 Mguanidine HCl concentrations were used. The full volume of the reagentswas loaded onto a borosilicate glass spin filter and incubated for 2minutes prior to centrifugation. The spin filter was centrifuged for 1minute at 10,000×g. The filter was then washed with 300 μL of washbuffer via 1 minute of centrifugation at 10,000×g. The spin filter wascentrifuged again for 2 minutes at 16,000×g to spin dry. The bound DNAfragments were incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 23 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples subjected to DNA binding solutions with differentguanidine HCl concentrations in the presence or absence of increasingamounts of DNA bind modifier (4.67 M tetramethyl ammonium acetate)during the binding reaction using borosilicate glass spin filters. DNAbinding solutions with 1.5 M and 3 M Guanidine HCl were used. In thisgel, the different DNA binding solutions was held constant at 170 μL andDNA sample was held constant at 50 μL.

Example 26: Effect of Different Concentrations of Diammonium Phosphate(DAP) on Size Selection of DNA on Borosilicate Glass Spin Filters

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of DNA binding buffer and0-35 μL of each DNA bind modifier. A control sample was made by mixingthe 50 μL DNA ladder and 170 μL of DNA binding buffer without DNA bindmodifier. Different dilutions of 4.03 M DAP (1-100%) were used as DNAbind modifiers. The full volume of the reagents was loaded onto aborosilicate glass spin filter and incubated for 2 minutes prior tocentrifugation. The spin filter was centrifuged for 1 minute at10,000×g. The filter was then washed with 500 μL of wash buffer via 1minute of centrifugation at 10,000×g. The spin filter was centrifugedagain for 2 minutes at 16,000×g to spin dry. The bound DNA fragmentswere incubated with 50 μL of elution buffer for 2 minutes andcentrifuged at 10,000×g for 1 minute to elute. The eluents were analyzedby agarose gel electrophoresis.

FIG. 24A compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof DNA binding solution and DAP amount was kept constant at 35 μL (DAPdilutions were varied from 1 to 100%).

FIG. 24B compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof nucleic acid binding solution and DAP amount was kept constant at 35μL (DAP dilutions were varied from 30 to 50%).

FIG. 24C compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the absence or presence of increasing amountsof diammonium phosphate (DAP) during the binding reaction usingborosilicate glass spin filters. Different dilutions of 4.03 M DAP wereused as DNA bind modifier. 50 μL of DNA ladder was combined with 170 μLof nucleic acid binding solution and DAP amount was kept constant at 35μL (DAP dilutions were varied from 25 to 100%).

Example 27: Effect of Increasing Concentrations of Different DNA BindModifiers on Size Selection of DNA on Silica-Coated Magnetic Beads

Fifty microliters of a nucleic acid-containing sample (e.g., diluted 1kb DNA molecular weight ladder) was mixed with 0-35 μL of DNA bindmodifier and 170 μL DNA binding buffer. 4.7 M tetramethyl ammoniumacetate and 2.02 M diammonium phosphate (DAP) were used as DNA bindmodifier. To the mixture, 25 μL of SwiftMag® beads was added and thesample was mixed with gentle vortexing every 2 minutes for a total of 10minutes. The reaction was placed on an appropriate magnet to collect theSwiftMag® beads for 2 minutes and the supernatant was removed. Thecollected beads were washed with 500 μL of wash buffer by repeatedlypipetting. The tubes were placed on the magnetic rack for 2 minutes andthe supernatant was removed. The tubes were incubated at 55 degreesCelsius, then 50 μL of elution buffer was added and the tubes wereincubated for 10 minutes (vortexing every 2 minutes). The eluent wastransferred to clean tubes and analyzed by agarose gel electrophoresis.

FIG. 25 compares electrophoretic separation of 1 kb DNA molecular weightladder samples contacted with silica-coated magnetic beads (SwiftMag®beads) in the presence or absence of DNA bind modifier. Differentamounts of 4.7 M tetramethyl ammonium acetate and 2.02 M diammoniumphosphate (DAP) were used as DNA bind modifier. 50 μL of DNA ladder wascombined with 170 μL DNA Binding Solution and 0-35 μL of DNA bindmodifier.

Example 28: Effect of Membrane Pretreatment with DNA Bind Modifier onSize Selection of DNA on Borosilicate Glass Spin Filters

To pretreat columns, the spin filters in Samples D and E were loadedwith a mixture of 35 μL of DNA bind modifier and 170 μL DNA bindingbuffer. 4.7 M tetramethyl ammonium acetate and 2.02 M diammoniumphosphate (DAP) were used as DNA bind modifiers. To pretreat columns forSamples F and G, spin filters were loaded with a 170 of DNA bindmodifier. The solutions were incubated with the spin filter for 2minutes then centrifuged for 1 minute at 10,000×g.

Fifty microliters of a nucleic acid-containing sample (diluted 1 kb DNAmolecular weight ladder) was mixed with 170 μL of different DNA bindingbuffers in the presence or absence of 35 μL of DNA bind modifier. Thissolution was loaded onto to either non-pretreated spin filters forSamples B and C, or to each of the pretreated spin filters for SamplesD, E, F, and G. The solutions were incubated for 2 minutes thencentrifuged for 1 minute at 10,000×g. The filter was then washed with500 μL of wash buffer via 1 minute of centrifugation at 10,000×g. Thespin filter was centrifuged again for 2 minutes at 16,000×g to spin dry.The bound DNA fragments were incubated with 50 μL of elution buffer for2 minutes and centrifuged at 10,000×g for 1 minute to elute. The eluentswere analyzed by agarose gel electrophoresis.

FIG. 26 compares the electrophoretic separation of 1 kb DNA molecularweight ladder samples in the presence or absence of DNA bind modifierduring the binding reaction using borosilicate glass spin filters withor without pretreatment with the DNA bind modifier. 4.7 M tetramethylammonium acetate and 2.02 M diammonium phosphate (DAP) were used as DNAbind modifiers. Sample A was a control sample that did not contain DNAbind modifier. 50 μL of DNA ladder was combined with 170 μL of DNAbinding solution and 35 μL of DNA bind modifier in Samples B and C. InSamples D and E, a mixture of 50 μL of DNA ladder, 170 μL of DNA bindingsolution, and 35 μL of the indicated DNA bind modifier was subjected toa spin filter pretreated with 35 μL of the same DNA bind modifier and170 μL DNA binding solution. In Samples F and G, a mixture of 50 μL ofDNA ladder, 170 μL of DNA binding solution, and 35 μL of the indicatedDNA bind modifier was subjected to a spin filter pretreated with 170 ofthe same DNA bind modifier.

1. A method of selectively isolating target nucleic acid molecules froma nucleic acid-containing sample, wherein the target nucleic acidmolecules are within a particular molecular size range and non-targetnucleic acid molecules are outside the molecular size range, comprising:contacting a sample comprising nucleic acid molecules with a matrix inthe presence of a small-molecule modulator, wherein the small-moleculemodulator is present in sufficient concentration that the target nucleicacid molecules selectively bind to the matrix and non-target nucleicacid molecules do not bind to the matrix.
 2. The method of claim 1,wherein greater than about 95% wt. % of the nucleic acid molecules boundto the matrix are the target nucleic acid molecules.
 3. The method ofclaim 1, wherein greater than about 90% wt. % of the nucleic acidmolecules bound to the matrix are the target nucleic acid molecules. 4.The method of claim 1, wherein greater than about 70% wt. % of thenucleic acid molecules bound to the matrix are the target nucleic acidmolecules.
 5. The method of claim 1, further comprising a step whereinthe matrix is washed to remove the unbound nucleic acid.
 6. The methodof claim 1, further comprising a step wherein the bound nucleic acidmolecules are eluted from the matrix.
 7. The method of claim 1, whereinthe matrix comprises silica.
 8. The method of claim 1, wherein thematrix comprises borosilicate glass.
 9. The method of claim 1 whereinthe matrix comprises silicon dioxide.
 10. The method of claim 1, whereinthe matrix comprises silicon dioxide-coated magnetic beads.
 11. Themethod of claim 1, wherein the matrix comprises a metal oxide.
 12. Themethod of claim 1, wherein the small-molecule modulator comprises acarboxylate moiety.
 13. The method of claim 1, wherein thesmall-molecule modulator comprises a phosphate, phosphonate, or boratemoiety.
 14. The method of claim 1, wherein the small-molecule modulatorcomprises an ammonium or substituted ammonium moiety.
 15. The method ofclaim 1, wherein the small-molecule modulator is of formula (Ia)

wherein R¹ is a structural moiety that satisfies the following twoconditions: 1) R¹ does not render the carboxylate insoluble in water athigh concentration (preferably 1-8 M); and 2) R¹ cannot be ionized to anegative species within the range of pH 4-9; M is a metal or N(R^(a))₄;each R^(a) is independently H or alkyl; and n is 1, 2, or 3; or ahydrate thereof.
 16. The method of claim 1, wherein the small-moleculemodulator is of formula (Ib)

wherein R² is a phosphate or a phosphonic acid; M is a metal orN(R^(a))₄; each R^(a) is independently H or alkyl; and n is 1, 2, or 3;or a hydrate thereof.
 17. The method of claim 1, wherein thesmall-molecule modulator is a carboxylate compound of formula (I)

wherein R is selected from the group consisting of H, substituted orunsubstituted C₁-C₈ alkyl, substituted or unsubstituted C₁-C₈ alkenyl,and substituted or unsubstituted C₁-C₈ alkynyl; M is a metal orN(R^(a))₄; each R^(a) is independently H or alkyl; and n is 1, 2, or 3;or a hydrate thereof.
 18. The method of claim 17, wherein R issubstituted or unsubstituted C₁-C₈ alkyl.
 19. The method of claim 18,wherein R is CH₃.
 20. The method of claim 17, wherein R is C₁-C₈ alkylsubstituted with one or more halogen.
 21. The method of claim 15,wherein M^(n+) is Na⁺, Li⁺, K+, Ca²⁺, Mg²⁺, Al³⁺, or NH₄ ⁺.
 22. Themethod of claim 1, wherein the small-molecule modulator comprisesacetate.
 23. The method of claim 1, wherein the small-molecule modulatoris ammonium acetate or sodium acetate.
 24. The method of claim 1,wherein the small-molecule modulator is in a solution.
 25. The method ofclaim 1, wherein the solution further comprises guanidine hydrochloride,Tris-HCl, and isopropanol.
 26. The method of claim 1, wherein thenucleic acid comprises DNA.
 27. The method of claim 1, wherein thenucleic acid comprises RNA.
 28. A method of selectively isolating targetnucleic acid molecules from a nucleic acid-containing sample, whereinthe target nucleic acid molecules are within a particular molecular sizerange and non-target nucleic acid molecules are outside the molecularsize range, comprising: a) contacting a sample comprising nucleic acidmolecules with a first matrix in the presence of a first small-moleculemodulator, wherein the first small-molecule modulator is present insufficient concentration that nucleic acid molecules of molecular sizeabove the upper limit of the target molecular size range selectivelybind to the first matrix and nucleic acid molecules of molecular sizebelow the upper limit of the target molecular size range do not bind tothe first matrix; b) collecting all or a portion of the sample that isnot bound to the first matrix; c) contacting all or the portion of thesample that is not bound to the first matrix with a second matrix in thepresence of a second small-molecule modulator, wherein the secondsmall-molecule modulator is present in a sufficient concentration thatnucleic acid molecules of the target molecular size range selectivelybind to the second matrix and nucleic acid molecules of molecular sizebelow the lower limit of the target molecular size range do not bind tothe second matrix.
 29. The method of claim 28, wherein the firstsmall-molecule modulator is a carboxylate compound.
 30. The method ofclaim 28, wherein the second small-molecule modulator is a carboxylatecompound.
 31. The method of claim 28, wherein the concentration of thefirst small-molecule modulator is greater than the concentration of thesecond small-molecule modulator.
 32. The method of claim 28, wherein thenucleic acid molecules of molecular size above the upper limit of thetarget molecular size range are removed from the first matrix by washingor elution to produce the second matrix.
 33. A method of selectivelyisolating target nucleic acid molecules from a nucleic acid-containingsample, wherein the target nucleic acid molecules are within aparticular molecular size range and non-target nucleic acid moleculesare outside the molecular size range, comprising: a) contacting a samplecomprising nucleic acid molecules with a first matrix in the absence ofa small-molecule modulator such that both target and non-target nucleicacid molecules bind to the matrix; b) washing the matrix in the presenceof a first small-molecule modulator, wherein the first small-moleculemodulator is present in sufficient concentration that nucleic acidmolecules of molecular size above the upper limit of the targetmolecular size range are selectively retained on the first matrix andnucleic acid molecules of molecular size below the upper limit of thetarget molecular size range are released from the first matrix; c)collecting all or a portion of the sample that is released from thefirst matrix; d) contacting all or the portion of the sample that isreleased from the first matrix with a second matrix in the presence of asecond small-molecule modulator, wherein the second small-moleculemodulator is present in a sufficient concentration that nucleic acidmolecules of the target molecular size range selectively bind to thesecond matrix and nucleic acid molecules of molecular size below thelower limit of the target molecular size range do not bind to the secondmatrix.
 34. The method of claim 33, wherein the first small-moleculemodulator is a carboxylate compound.
 35. The method of claim 33, whereinthe second small-molecule modulator is a carboxylate compound.
 36. Themethod of claim 33, wherein the concentration of the firstsmall-molecule modulator is greater than the concentration of the secondsmall-molecule modulator.
 37. A kit comprising a small-moleculemodulator, a matrix, and instructions for use according to the method ofclaim
 1. 38. The kit of claim 37, wherein the small-molecule modulatoris a carboxylate compound.
 39. A kit comprising ammonium acetate,guanidine hydrochloride, and Tris HCl.
 40. The kit of claim 39, wherethe ammonium acetate, guanidine hydrochloride, and Tris HCl are presentin a solution.
 41. The kit of claim 39, comprising about 7.5 M ammoniumacetate, about 5.2 M guanidine hydrochloride, about 30 mM Tris HCl. 42.The kit of claim 39, further comprising a matrix.
 43. The kit of claim39, further comprising isopropanol.
 44. The kit of claim 39, furthercomprising instructions for use according to claim 1.